diff --git a/DESCRIPTION b/DESCRIPTION
index 658a283..c42891d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: sigurd
 Type: Package
 Title: Single cell Genotyping Using RNA Data
-Version: 0.3.1
+Version: 0.3.2
 Authors@R: c(
   person(given = "Martin",
          family = "Grasshoff",
diff --git a/README.md b/README.md
index c07a85c..8e69089 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,7 @@ The mutation data was obtained from the Sanger Institute Catalogue Of Somatic Mu
 
 ```
 
-# Current Features v0.3.1
+# Current Features v0.3.2
 
 - Loading data from VarTrix and MAEGATK.
 - Transforming the data to be compatible for joint analysis.
diff --git a/docs/404.html b/docs/404.html
index 31a38d7..b89edbf 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -8,53 +8,58 @@
 <title>Page not found (404) • sigurd</title>
 <script src="https://costalab.github.io/sigurd/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<script src="https://costalab.github.io/sigurd/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
 </head>
 <body>
     <a href="https://costalab.github.io/sigurd/#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
-
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="https://costalab.github.io/sigurd/index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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+    
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+<li class="nav-item">
+  <a class="nav-link" href="https://costalab.github.io/sigurd/reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
-<li><a class="dropdown-item" href="https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="https://costalab.github.io/sigurd/articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
-  </ul>
+  <a href="https://costalab.github.io/sigurd/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="https://costalab.github.io/sigurd/articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
 </li>
       </ul>
-<ul class="navbar-nav">
-<li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
-</form></li>
-      </ul>
-</div>
+<form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
+</form>
 
+      <ul class="navbar-nav"></ul>
+</div>
 
+    
   </div>
 </nav><div class="container template-title-body">
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   <main id="main" class="col-md-9"><div class="page-header">
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+      
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 Content not found. Please use links in the navbar.
@@ -64,19 +69,21 @@ <h1>Page not found (404)</h1>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p>
+<p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+  
 
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diff --git a/docs/articles/BoneMarrow_SIGURD.html b/docs/articles/BoneMarrow_SIGURD.html
index c73e856..f2b82c5 100644
--- a/docs/articles/BoneMarrow_SIGURD.html
+++ b/docs/articles/BoneMarrow_SIGURD.html
@@ -5,59 +5,66 @@
 <meta charset="utf-8">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
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+    
 
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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+<li class="nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="active nav-item dropdown">
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+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
 </li>
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-<ul class="navbar-nav">
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
-</form></li>
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+<form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
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-
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+      <img src="" class="logo" alt=""><h1>Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</h1>
             
       
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+      
       <div class="d-none name"><code>BoneMarrow_SIGURD.Rmd</code></div>
     </div>
 
@@ -143,7 +150,7 @@ <h2 id="cell-type-enrichment-2593ga">Cell Type Enrichment 2593G&gt;A<a class="an
 <pre><code><span><span class="co">## [1] "We get a count matrix of the chrM_2593_G_A per CellType."</span></span></code></pre>
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">ComplexHeatmap</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html" class="external-link">Heatmap</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="va">result_enrichment</span><span class="op">$</span><span class="va">Heatmap_Values</span><span class="op">)</span>, cluster_rows <span class="op">=</span> <span class="cn">FALSE</span>, cluster_columns <span class="op">=</span> <span class="cn">FALSE</span>, col<span class="op">=</span> <span class="fu">circlize</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/circlize/man/colorRamp2.html" class="external-link">colorRamp2</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">result_enrichment</span><span class="op">$</span><span class="va">Heatmap_Values</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"white"</span>, <span class="st">"red"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
-<p><img src="BoneMarrow_SIGURD_files/figure-html/unnamed-chunk-3-1.png" width="700"></p>
+<p><img src="BoneMarrow_SIGURD_files/figure-html/unnamed-chunk-3-1.png" width="576"></p>
 </div>
 <div class="section level2">
 <h2 id="cell-type-enrichment-6243ga">Cell Type Enrichment 6243G&gt;A<a class="anchor" aria-label="anchor" href="#cell-type-enrichment-6243ga"></a>
@@ -342,26 +349,28 @@ <h2 id="enrichment-with-somatic-variants">Enrichment with somatic variants<a cla
 </tbody>
 </table>
 </div>
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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@@ -155,26 +162,28 @@ <h2 id="visualisation-using-sigurd-1">Visualisation using SIGURD<a class="anchor
 <span><span class="fu"><a href="../reference/HeatmapVoi.html">HeatmapVoi</a></span><span class="op">(</span>SE <span class="op">=</span> <span class="va">genotyping</span>, voi <span class="op">=</span> <span class="va">voi.ch.lineages</span>, minimum_coverage <span class="op">=</span> <span class="fl">3</span>, sort_cells <span class="op">=</span> <span class="cn">TRUE</span>, cluster_variants <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
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       <div class="d-none name"><code>TenX_CellMixture_SIGURD.Rmd</code></div>
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@@ -155,26 +162,28 @@ <h2 id="selecting-variants-with-comparatively-high-vaf-between-groups">Selecting
 <span><span class="fu"><a href="../reference/HeatmapVoi.html">HeatmapVoi</a></span><span class="op">(</span>SE <span class="op">=</span> <span class="va">genotyping</span>, voi <span class="op">=</span> <span class="va">voi.ch.lineages</span>, minimum_coverage <span class="op">=</span> <span class="fl">3</span>, sort_cells <span class="op">=</span> <span class="cn">TRUE</span>, cluster_variants <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
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diff --git a/docs/articles/TenX_CellMixture_SIGURD_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/TenX_CellMixture_SIGURD_files/figure-html/unnamed-chunk-5-1.png
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       <dl><dt><a href="BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></dt>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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+    <a class="dropdown-item" href="articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
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-    <div class="section level2">
+    <div class="section level2 citation">
       <h2>Authors</h2>
-
+      
       <ul class="list-unstyled"><li>
-          <p><strong>Martin Grasshoff</strong>. Author, maintainer.
+          <p><strong>Martin Grasshoff</strong>. Author, maintainer. 
           </p>
         </li>
         <li>
@@ -49,13 +56,13 @@ <h2>Authors</h2>
         </li>
       </ul></div>
 
-    <div class="section level2">
+    <div class="section level2 citation">
       <h2 id="citation">Citation</h2>
       <p></p>
 
       <p>Grasshoff M, Costa I (2024).
 <em>sigurd: Single cell Genotyping Using RNA Data</em>.
-R package version 0.3.1, <a href="https://costalab.github.io/sigurd/">https://costalab.github.io/sigurd/</a>.
+R package version 0.3.1, <a href="https://costalab.github.io/sigurd/">https://costalab.github.io/sigurd/</a>. 
 </p>
       <pre>@Manual{,
   title = {sigurd: Single cell Genotyping Using RNA Data},
@@ -65,24 +72,23 @@ <h2 id="citation">Citation</h2>
   url = {https://costalab.github.io/sigurd/},
 }</pre>
     </div>
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-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
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transparent;--bs-gradient: none}.btn-outline-light{--bs-btn-color: #f8f9fa;--bs-btn-border-color: #f8f9fa;--bs-btn-hover-color: #000;--bs-btn-hover-bg: #f8f9fa;--bs-btn-hover-border-color: #f8f9fa;--bs-btn-focus-shadow-rgb: 248,249,250;--bs-btn-active-color: #000;--bs-btn-active-bg: #f8f9fa;--bs-btn-active-border-color: #f8f9fa;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #f8f9fa;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #f8f9fa;--bs-btn-bg: transparent;--bs-gradient: none}.btn-outline-dark{--bs-btn-color: #212529;--bs-btn-border-color: #212529;--bs-btn-hover-color: #fff;--bs-btn-hover-bg: #212529;--bs-btn-hover-border-color: #212529;--bs-btn-focus-shadow-rgb: 33,37,41;--bs-btn-active-color: #fff;--bs-btn-active-bg: #212529;--bs-btn-active-border-color: #212529;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #212529;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: 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10rem;--bs-dropdown-padding-x: 0;--bs-dropdown-padding-y: .5rem;--bs-dropdown-spacer: .125rem;--bs-dropdown-font-size:1rem;--bs-dropdown-color: var(--bs-body-color);--bs-dropdown-bg: var(--bs-body-bg);--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-border-radius: var(--bs-border-radius);--bs-dropdown-border-width: var(--bs-border-width);--bs-dropdown-inner-border-radius: calc(var(--bs-border-radius) - var(--bs-border-width));--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-divider-margin-y: .5rem;--bs-dropdown-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15);--bs-dropdown-link-color: var(--bs-body-color);--bs-dropdown-link-hover-color: var(--bs-body-color);--bs-dropdown-link-hover-bg: var(--bs-tertiary-bg);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #0d6efd;--bs-dropdown-link-disabled-color: var(--bs-tertiary-color);--bs-dropdown-item-padding-x: 1rem;--bs-dropdown-item-padding-y: .25rem;--bs-dropdown-header-color: #6c757d;--bs-dropdown-header-padding-x: 1rem;--bs-dropdown-header-padding-y: .5rem;position:absolute;z-index:var(--bs-dropdown-zindex);display:none;min-width:var(--bs-dropdown-min-width);padding:var(--bs-dropdown-padding-y) var(--bs-dropdown-padding-x);margin:0;font-size:var(--bs-dropdown-font-size);color:var(--bs-dropdown-color);text-align:left;list-style:none;background-color:var(--bs-dropdown-bg);background-clip:padding-box;border:var(--bs-dropdown-border-width) solid var(--bs-dropdown-border-color);border-radius:var(--bs-dropdown-border-radius)}.dropdown-menu[data-bs-popper]{top:100%;left:0;margin-top:var(--bs-dropdown-spacer)}.dropdown-menu-start{--bs-position: start}.dropdown-menu-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-end{--bs-position: end}.dropdown-menu-end[data-bs-popper]{right:0;left:auto}@media (min-width: 576px){.dropdown-menu-sm-start{--bs-position: start}.dropdown-menu-sm-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-sm-end{--bs-position: end}.dropdown-menu-sm-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 768px){.dropdown-menu-md-start{--bs-position: start}.dropdown-menu-md-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-md-end{--bs-position: end}.dropdown-menu-md-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 992px){.dropdown-menu-lg-start{--bs-position: start}.dropdown-menu-lg-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-lg-end{--bs-position: end}.dropdown-menu-lg-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 1200px){.dropdown-menu-xl-start{--bs-position: start}.dropdown-menu-xl-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-xl-end{--bs-position: end}.dropdown-menu-xl-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 1400px){.dropdown-menu-xxl-start{--bs-position: start}.dropdown-menu-xxl-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-xxl-end{--bs-position: end}.dropdown-menu-xxl-end[data-bs-popper]{right:0;left:auto}}.dropup .dropdown-menu[data-bs-popper]{top:auto;bottom:100%;margin-top:0;margin-bottom:var(--bs-dropdown-spacer)}.dropup .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:"";border-top:0;border-right:.3em solid transparent;border-bottom:.3em solid;border-left:.3em solid transparent}.dropup .dropdown-toggle:empty::after{margin-left:0}.dropend .dropdown-menu[data-bs-popper]{top:0;right:auto;left:100%;margin-top:0;margin-left:var(--bs-dropdown-spacer)}.dropend .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:"";border-top:.3em solid transparent;border-right:0;border-bottom:.3em solid transparent;border-left:.3em solid}.dropend .dropdown-toggle:empty::after{margin-left:0}.dropend .dropdown-toggle::after{vertical-align:0}.dropstart .dropdown-menu[data-bs-popper]{top:0;right:100%;left:auto;margin-top:0;margin-right:var(--bs-dropdown-spacer)}.dropstart .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:""}.dropstart .dropdown-toggle::after{display:none}.dropstart .dropdown-toggle::before{display:inline-block;margin-right:.255em;vertical-align:.255em;content:"";border-top:.3em solid transparent;border-right:.3em solid;border-bottom:.3em solid transparent}.dropstart .dropdown-toggle:empty::after{margin-left:0}.dropstart .dropdown-toggle::before{vertical-align:0}.dropdown-divider{height:0;margin:var(--bs-dropdown-divider-margin-y) 0;overflow:hidden;border-top:1px solid var(--bs-dropdown-divider-bg);opacity:1}.dropdown-item{display:block;width:100%;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);clear:both;font-weight:400;color:var(--bs-dropdown-link-color);text-align:inherit;text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;white-space:nowrap;background-color:transparent;border:0;border-radius:var(--bs-dropdown-item-border-radius, 0)}.dropdown-item:hover,.dropdown-item:focus{color:var(--bs-dropdown-link-hover-color);background-color:var(--bs-dropdown-link-hover-bg)}.dropdown-item.active,.dropdown-item:active{color:var(--bs-dropdown-link-active-color);text-decoration:none;background-color:var(--bs-dropdown-link-active-bg)}.dropdown-item.disabled,.dropdown-item:disabled{color:var(--bs-dropdown-link-disabled-color);pointer-events:none;background-color:transparent}.dropdown-menu.show{display:block}.dropdown-header{display:block;padding:var(--bs-dropdown-header-padding-y) var(--bs-dropdown-header-padding-x);margin-bottom:0;font-size:.875rem;color:var(--bs-dropdown-header-color);white-space:nowrap}.dropdown-item-text{display:block;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color: #dee2e6;--bs-dropdown-bg: #343a40;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color: #dee2e6;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #0d6efd;--bs-dropdown-link-disabled-color: #adb5bd;--bs-dropdown-header-color: #adb5bd}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:var(--bs-border-radius)}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem rgba(13,110,253,0.25)}.nav-link.disabled,.nav-link:disabled{color:var(--bs-nav-link-disabled-color);pointer-events:none;cursor:default}.nav-tabs{--bs-nav-tabs-border-width: var(--bs-border-width);--bs-nav-tabs-border-color: var(--bs-border-color);--bs-nav-tabs-border-radius: var(--bs-border-radius);--bs-nav-tabs-link-hover-border-color: var(--bs-secondary-bg) var(--bs-secondary-bg) var(--bs-border-color);--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * var(--bs-nav-tabs-border-width));border-top-left-radius:0;border-top-right-radius:0}.nav-pills{--bs-nav-pills-border-radius: var(--bs-border-radius);--bs-nav-pills-link-active-color: #fff;--bs-nav-pills-link-active-bg: #0d6efd}.nav-pills .nav-link{border-radius:var(--bs-nav-pills-border-radius)}.nav-pills .nav-link.active,.nav-pills .show>.nav-link{color:var(--bs-nav-pills-link-active-color);background-color:var(--bs-nav-pills-link-active-bg)}.nav-underline{--bs-nav-underline-gap: 1rem;--bs-nav-underline-border-width: .125rem;--bs-nav-underline-link-active-color: var(--bs-emphasis-color);gap:var(--bs-nav-underline-gap)}.nav-underline .nav-link{padding-right:0;padding-left:0;border-bottom:var(--bs-nav-underline-border-width) solid transparent}.nav-underline .nav-link:hover,.nav-underline .nav-link:focus{border-bottom-color:currentcolor}.nav-underline .nav-link.active,.nav-underline .show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;-webkit-flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified .nav-item{flex-basis:0;-webkit-flex-basis:0;flex-grow:1;-webkit-flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x: 0;--bs-navbar-padding-y: .5rem;--bs-navbar-color: rgba(var(--bs-emphasis-color-rgb), 0.65);--bs-navbar-hover-color: rgba(var(--bs-emphasis-color-rgb), 0.8);--bs-navbar-disabled-color: rgba(var(--bs-emphasis-color-rgb), 0.3);--bs-navbar-active-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-padding-y: .3125rem;--bs-navbar-brand-margin-end: 1rem;--bs-navbar-brand-font-size: 1.25rem;--bs-navbar-brand-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-hover-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-nav-link-padding-x: .5rem;--bs-navbar-toggler-padding-y: .25rem;--bs-navbar-toggler-padding-x: .75rem;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%2833,37,41,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(var(--bs-emphasis-color-rgb), 0.15);--bs-navbar-toggler-border-radius: var(--bs-border-radius);--bs-navbar-toggler-focus-width: .25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) 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var(--bs-navbar-hover-color);--bs-nav-link-disabled-color: var(--bs-navbar-disabled-color);display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;list-style:none}.navbar-nav .nav-link.active,.navbar-nav .nav-link.show{color:var(--bs-navbar-active-color)}.navbar-nav .dropdown-menu{position:static}.navbar-text{padding-top:.5rem;padding-bottom:.5rem;color:var(--bs-navbar-color)}.navbar-text a,.navbar-text a:hover,.navbar-text a:focus{color:var(--bs-navbar-active-color)}.navbar-collapse{flex-basis:100%;-webkit-flex-basis:100%;flex-grow:1;-webkit-flex-grow:1;align-items:center;-webkit-align-items:center}.navbar-toggler{padding:var(--bs-navbar-toggler-padding-y) var(--bs-navbar-toggler-padding-x);font-size:var(--bs-navbar-toggler-font-size);line-height:1;color:var(--bs-navbar-color);background-color:transparent;border:var(--bs-border-width) solid 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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!important;transform:none !important;transition:none}.navbar-expand-xl .offcanvas .offcanvas-header{display:none}.navbar-expand-xl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 1400px){.navbar-expand-xxl{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-xxl .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-xxl .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-xxl .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-xxl .navbar-nav-scroll{overflow:visible}.navbar-expand-xxl .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-xxl .navbar-toggler{display:none}.navbar-expand-xxl .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand .navbar-toggler{display:none}.navbar-expand .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand .offcanvas .offcanvas-header{display:none}.navbar-expand .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}.navbar-dark,.navbar[data-bs-theme="dark"]{--bs-navbar-color: rgba(var(--bs-emphasis-color-rgb), 0.55);--bs-navbar-hover-color: rgba(var(--bs-emphasis-color-rgb), 0.75);--bs-navbar-disabled-color: rgba(var(--bs-emphasis-color-rgb), 0.25);--bs-navbar-active-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-hover-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-toggler-border-color: rgba(var(--bs-emphasis-color-rgb), 0.1);--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme="dark"] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: .5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width: var(--bs-border-width);--bs-card-border-color: var(--bs-border-color-translucent);--bs-card-border-radius: var(--bs-border-radius);--bs-card-box-shadow: ;--bs-card-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-card-cap-padding-y: .5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(var(--bs-body-color-rgb), 0.03);--bs-card-cap-color: ;--bs-card-height: ;--bs-card-color: ;--bs-card-bg: var(--bs-body-bg);--bs-card-img-overlay-padding: 1rem;--bs-card-group-margin: .75rem;position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;min-width:0;height:var(--bs-card-height);color:var(--bs-body-color);word-wrap:break-word;background-color:var(--bs-card-bg);background-clip:border-box;border:var(--bs-card-border-width) solid var(--bs-card-border-color);border-radius:var(--bs-card-border-radius)}.card>hr{margin-right:0;margin-left:0}.card>.list-group{border-top:inherit;border-bottom:inherit}.card>.list-group:first-child{border-top-width:0;border-top-left-radius:var(--bs-card-inner-border-radius);border-top-right-radius:var(--bs-card-inner-border-radius)}.card>.list-group:last-child{border-bottom-width:0;border-bottom-right-radius:var(--bs-card-inner-border-radius);border-bottom-left-radius:var(--bs-card-inner-border-radius)}.card>.card-header+.list-group,.card>.list-group+.card-footer{border-top:0}.card-body{flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-card-spacer-y) var(--bs-card-spacer-x);color:var(--bs-card-color)}.card-title{margin-bottom:var(--bs-card-title-spacer-y);color:var(--bs-card-title-color)}.card-subtitle{margin-top:calc(-.5 * var(--bs-card-title-spacer-y));margin-bottom:0;color:var(--bs-card-subtitle-color)}.card-text:last-child{margin-bottom:0}.card-link+.card-link{margin-left:var(--bs-card-spacer-x)}.card-header{padding:var(--bs-card-cap-padding-y) var(--bs-card-cap-padding-x);margin-bottom:0;color:var(--bs-card-cap-color);background-color:var(--bs-card-cap-bg);border-bottom:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card-header:first-child{border-radius:var(--bs-card-inner-border-radius) var(--bs-card-inner-border-radius) 0 0}.card-footer{padding:var(--bs-card-cap-padding-y) var(--bs-card-cap-padding-x);color:var(--bs-card-cap-color);background-color:var(--bs-card-cap-bg);border-top:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card-footer:last-child{border-radius:0 0 var(--bs-card-inner-border-radius) var(--bs-card-inner-border-radius)}.card-header-tabs{margin-right:calc(-.5 * var(--bs-card-cap-padding-x));margin-bottom:calc(-1 * 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wrap;-webkit-flex-flow:row wrap}.card-group>.card{flex:1 0 0%;-webkit-flex:1 0 0%;margin-bottom:0}.card-group>.card+.card{margin-left:0;border-left:0}.card-group>.card:not(:last-child){border-top-right-radius:0;border-bottom-right-radius:0}.card-group>.card:not(:last-child) .card-img-top,.card-group>.card:not(:last-child) .card-header{border-top-right-radius:0}.card-group>.card:not(:last-child) .card-img-bottom,.card-group>.card:not(:last-child) .card-footer{border-bottom-right-radius:0}.card-group>.card:not(:first-child){border-top-left-radius:0;border-bottom-left-radius:0}.card-group>.card:not(:first-child) .card-img-top,.card-group>.card:not(:first-child) .card-header{border-top-left-radius:0}.card-group>.card:not(:first-child) .card-img-bottom,.card-group>.card:not(:first-child) .card-footer{border-bottom-left-radius:0}}.accordion{--bs-accordion-color: var(--bs-body-color);--bs-accordion-bg: var(--bs-body-bg);--bs-accordion-transition: color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out,border-radius 0.15s ease;--bs-accordion-border-color: var(--bs-border-color);--bs-accordion-border-width: var(--bs-border-width);--bs-accordion-border-radius: var(--bs-border-radius);--bs-accordion-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-accordion-btn-padding-x: 1.25rem;--bs-accordion-btn-padding-y: 1rem;--bs-accordion-btn-color: var(--bs-body-color);--bs-accordion-btn-bg: var(--bs-accordion-bg);--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23212529'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-icon-width: 1.25rem;--bs-accordion-btn-icon-transform: rotate(-180deg);--bs-accordion-btn-icon-transition: transform 0.2s ease-in-out;--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23052c65'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #86b7fe;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(13,110,253,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1 * var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%236ea8fe'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%236ea8fe'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(13,110,253,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #0d6efd;--bs-pagination-active-border-color: #0d6efd;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #0d6efd;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #0d6efd;--bs-list-group-active-border-color: #0d6efd;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") 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var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * 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576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 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var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: 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var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(13,110,253,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme="dark"] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * 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.dropdown-toggle::after{vertical-align:0}.dropstart .dropdown-menu[data-bs-popper]{top:0;right:100%;left:auto;margin-top:0;margin-right:var(--bs-dropdown-spacer)}.dropstart .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:""}.dropstart .dropdown-toggle::after{display:none}.dropstart .dropdown-toggle::before{display:inline-block;margin-right:.255em;vertical-align:.255em;content:"";border-top:.3em solid transparent;border-right:.3em solid;border-bottom:.3em solid transparent}.dropstart .dropdown-toggle:empty::after{margin-left:0}.dropstart .dropdown-toggle::before{vertical-align:0}.dropdown-divider{height:0;margin:var(--bs-dropdown-divider-margin-y) 0;overflow:hidden;border-top:1px solid var(--bs-dropdown-divider-bg);opacity:1}.dropdown-item{display:block;width:100%;padding:var(--bs-dropdown-item-padding-y) 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var(--bs-dropdown-header-padding-x);margin-bottom:0;font-size:.875rem;color:var(--bs-dropdown-header-color);white-space:nowrap}.dropdown-item-text{display:block;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color: #dee2e6;--bs-dropdown-bg: #343A46;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color: #dee2e6;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #007bc2;--bs-dropdown-link-disabled-color: #8D959E;--bs-dropdown-header-color: #8D959E}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:var(--bs-border-radius)}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:1.5em;padding-left:1.5em}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * 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var(--bs-border-color);--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * 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1);--bs-navbar-brand-hover-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-nav-link-padding-x: .5rem;--bs-navbar-toggler-padding-y: .25rem;--bs-navbar-toggler-padding-x: .75rem;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%2829,31,33,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(var(--bs-emphasis-color-rgb), 0.15);--bs-navbar-toggler-border-radius: var(--bs-border-radius);--bs-navbar-toggler-focus-width: .25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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!important;transform:none !important;transition:none}.navbar-expand-xl .offcanvas .offcanvas-header{display:none}.navbar-expand-xl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 1400px){.navbar-expand-xxl{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-xxl .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-xxl .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-xxl .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-xxl .navbar-nav-scroll{overflow:visible}.navbar-expand-xxl .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-xxl .navbar-toggler{display:none}.navbar-expand-xxl .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand .navbar-toggler{display:none}.navbar-expand .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand .offcanvas .offcanvas-header{display:none}.navbar-expand .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}.navbar-dark,.navbar[data-bs-theme="dark"]{--bs-navbar-color: rgba(var(--bs-emphasis-color-rgb), 0.55);--bs-navbar-hover-color: rgba(var(--bs-emphasis-color-rgb), 0.75);--bs-navbar-disabled-color: rgba(var(--bs-emphasis-color-rgb), 0.25);--bs-navbar-active-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-hover-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-toggler-border-color: rgba(var(--bs-emphasis-color-rgb), 0.1);--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme="dark"] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: .5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width: var(--bs-border-width);--bs-card-border-color: var(--bs-border-color-translucent);--bs-card-border-radius: 8px;--bs-card-box-shadow: ;--bs-card-inner-border-radius: calc(8px - (var(--bs-border-width)));--bs-card-cap-padding-y: .5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(var(--bs-body-color-rgb), 0.03);--bs-card-cap-color: ;--bs-card-height: ;--bs-card-color: ;--bs-card-bg: var(--bs-body-bg);--bs-card-img-overlay-padding: 1rem;--bs-card-group-margin: .75rem;position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;min-width:0;height:var(--bs-card-height);color:var(--bs-body-color);word-wrap:break-word;background-color:var(--bs-card-bg);background-clip:border-box;border:var(--bs-card-border-width) solid var(--bs-card-border-color);border-radius:var(--bs-card-border-radius)}.card>hr{margin-right:0;margin-left:0}.card>.list-group{border-top:inherit;border-bottom:inherit}.card>.list-group:first-child{border-top-width:0;border-top-left-radius:var(--bs-card-inner-border-radius);border-top-right-radius:var(--bs-card-inner-border-radius)}.card>.list-group:last-child{border-bottom-width:0;border-bottom-right-radius:var(--bs-card-inner-border-radius);border-bottom-left-radius:var(--bs-card-inner-border-radius)}.card>.card-header+.list-group,.card>.list-group+.card-footer{border-top:0}.card-body{flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-card-spacer-y) var(--bs-card-spacer-x);color:var(--bs-card-color)}.card-title{margin-bottom:var(--bs-card-title-spacer-y);color:var(--bs-card-title-color)}.card-subtitle{margin-top:calc(-.5 * 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wrap;-webkit-flex-flow:row wrap}.card-group>.card{flex:1 0 0%;-webkit-flex:1 0 0%;margin-bottom:0}.card-group>.card+.card{margin-left:0;border-left:0}.card-group>.card:not(:last-child){border-top-right-radius:0;border-bottom-right-radius:0}.card-group>.card:not(:last-child) .card-img-top,.card-group>.card:not(:last-child) .card-header{border-top-right-radius:0}.card-group>.card:not(:last-child) .card-img-bottom,.card-group>.card:not(:last-child) .card-footer{border-bottom-right-radius:0}.card-group>.card:not(:first-child){border-top-left-radius:0;border-bottom-left-radius:0}.card-group>.card:not(:first-child) .card-img-top,.card-group>.card:not(:first-child) .card-header{border-top-left-radius:0}.card-group>.card:not(:first-child) .card-img-bottom,.card-group>.card:not(:first-child) .card-footer{border-bottom-left-radius:0}}.accordion{--bs-accordion-color: var(--bs-body-color);--bs-accordion-bg: var(--bs-body-bg);--bs-accordion-transition: color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out,border-radius 0.15s ease;--bs-accordion-border-color: var(--bs-border-color);--bs-accordion-border-width: var(--bs-border-width);--bs-accordion-border-radius: var(--bs-border-radius);--bs-accordion-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-accordion-btn-padding-x: 1.25rem;--bs-accordion-btn-padding-y: 1rem;--bs-accordion-btn-color: var(--bs-body-color);--bs-accordion-btn-bg: var(--bs-accordion-bg);--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%231D1F21'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-icon-width: 1.25rem;--bs-accordion-btn-icon-transform: rotate(-180deg);--bs-accordion-btn-icon-transition: transform 0.2s ease-in-out;--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2300314e'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #80bde1;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(0,123,194,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: ;--bs-accordion-active-bg: }.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1 * var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2366b0da'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2366b0da'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(0,123,194,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #007bc2;--bs-pagination-active-border-color: #007bc2;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #007bc2;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #007bc2;--bs-list-group-active-border-color: #007bc2;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(0,123,194,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:3px;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme="dark"] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * 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var(--bs-card-border-color)}.popover{--bs-popover-shadow: 0px 1px 2px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 3px 7px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 12px 30px RGBA(var(--bslib-box-shadow-color-rgb), 0.08);box-shadow:var(--bs-popover-shadow)}:root{--bslib-dashboard-sidebar-bg: var(--bs-body-bg);--bslib-dashboard-sidebar-main-bg: var(--bs-body-bg);--bslib-dashboard-main-bg: rgb(247, 247, 247);--bs-card-border-color: var(--bslib-dashboard-border-color-translucent, var(--bs-border-color-translucent));--bslib-dashboard-card-header-font-weight: 600;--bslib-sidebar-bg: RGBA(var(--bs-body-bg-rgb), 0.05)}[data-bs-theme="dark"]{--bslib-dashboard-main-bg: rgb(20, 20, 24)}.bslib-card{--bs-card-cap-bg: }.bslib-card .card-header,.bslib-card .card-footer{font-size:0.9rem}.bslib-card 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.value-box-showcase>i.fab{background:linear-gradient(140deg, #007bc2 36%, #74149c 180%) #007bc2;-webkit-background-clip:text;-webkit-text-fill-color:transparent}.bslib-value-box.default .value-box-showcase>i.material-icons{background:linear-gradient(140deg, #007bc2 36%, #74149c 180%) #007bc2;-webkit-background-clip:text;-webkit-text-fill-color:transparent}.bslib-value-box.default .value-box-showcase>svg.bi{fill:url("#bslib---icon-gradient") #007bc2 !important}.bslib-value-box.default .value-box-showcase>svg.fa{fill:url("#bslib---icon-gradient") #007bc2 !important}.bslib-value-box.default .value-box-showcase>svg.fas{fill:url("#bslib---icon-gradient") #007bc2 !important}.bslib-value-box.default .value-box-showcase>svg.far{fill:url("#bslib---icon-gradient") #007bc2 !important}.bslib-value-box.default .value-box-showcase>svg.fab{fill:url("#bslib---icon-gradient") #007bc2 !important}.bslib-value-box.default .value-box-showcase>svg.material-icons{fill:url("#bslib---icon-gradient") #007bc2 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1rem);border:1px solid var(--bs-border-color-translucent);border-radius:8px;box-shadow:0px 1px 2px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 3px 7px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 12px 30px RGBA(var(--bslib-box-shadow-color-rgb), 0.08)}.shiny-notification.shiny-notification .shiny-notification-close{position:absolute;font-size:1.5em;width:2rem;height:2rem;top:0;right:0;bottom:unset;display:flex;align-items:center;justify-content:center;padding:0.25rem;cursor:pointer;font-weight:200;color:currentColor}.shiny-notification.shiny-notification .shiny-notification-close:hover{font-weight:normal}.shiny-notification.shiny-notification .shiny-notification-content-text :last-child{margin-bottom:0}.row>main{max-width:50rem}@media (min-width: 1200px) and (max-width: 1399.98px){.container .row{justify-content:space-evenly}}@media (min-width: 1400px){body{font-size:18px}.col-md-3{margin-left:5rem}}.navbar-nav .nav-item>.nav-link{border-radius:3px;padding:0.5rem}.navbar>.container{align-items:baseline;-webkit-align-items:baseline}.navbar-light .navbar-nav .active>.nav-link{background:#e9ecef;color:#1D1F21}.navbar-dark .navbar-nav .active>.nav-link{background:#343A46;color:#fff}.navbar-dark .navbar-nav .nav-item>.nav-link:hover,.navbar-light .navbar-nav .nav-item>.nav-link:hover{background:rgba(0,123,194,0.1)}.navbar-dark input[type="search"]{border-color:#707782;background-color:#1D1F21;color:#e9ecef}input[type="search"]{border-color:#dee2e6;width:12rem}.headroom{will-change:transform;transition:transform 400ms ease}.headroom--pinned{transform:translateY(0%)}.headroom--unpinned{transform:translateY(-100%)}.row>main,.row>aside{margin-top:56px}html,body{scroll-padding:56px}@media (min-width: 576px){#toc{position:sticky;top:56px;max-height:calc(100vh - 56px - 1rem);overflow-y:auto}}aside h2,aside .h2{margin-top:1.5rem;font-size:1.25rem}aside .roles{color:#4a4c4d}aside .list-unstyled 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.pkgdown-footer-right{text-align:right}}footer div{flex:1 1 auto}html,body{height:100%}body>.container{min-height:100%;display:flex;flex-direction:column}body>.container .row{flex:1 0 auto}::selection{background-color:#cce5f3}main img{max-width:100%;height:auto}main table{display:block;overflow:auto}body{font-display:fallback}.page-header{border-bottom:1px solid #dee2e6;padding-bottom:0.5rem;margin-bottom:0.5rem;margin-top:1.5rem}dd{margin-left:1.5rem}summary{margin-bottom:0.5rem}details{margin-bottom:1rem}.html-widget{margin-bottom:1rem}a.anchor{display:none;margin-left:5px;width:Min(0.9em, 20px);height:Min(0.9em, 20px);background-image:url(../../link.svg);background-repeat:no-repeat;background-size:Min(0.9em, 20px) Min(0.9em, 20px);background-position:center center}h2:hover .anchor,.h2:hover .anchor,h3:hover .anchor,.h3:hover .anchor,h4:hover .anchor,.h4:hover .anchor,h5:hover .anchor,.h5:hover .anchor,h6:hover .anchor,.h6:hover .anchor{display:inline-block}.orcid{color:#A6CE39;margin-right:4px}.fab{font-family:"Font Awesome 5 Brands" !important}img.logo{float:right;width:100px;margin-left:30px}.template-home img.logo{width:120px}@media (max-width: 575.98px){img.logo{width:80px}}@media (min-width: 576px){.page-header{min-height:88px}.template-home .page-header{min-height:104px}}.line-block{margin-bottom:1rem}.template-reference-index dt{font-weight:normal}.template-reference-index code{word-wrap:normal}.icon{float:right}.icon img{width:40px}a.footnote-ref{cursor:pointer}.popover{width:Min(100vw, 32rem);font-size:0.9rem;box-shadow:4px 4px 8px rgba(0,0,0,0.3)}.popover-body{padding:0.75rem}.popover-body p:last-child{margin-bottom:0}.tab-content{padding:1rem}.tabset-pills .tab-content{border:solid 1px #e5e5e5}.tab-content{display:flex}.tab-content>.tab-pane{display:block;visibility:hidden;margin-right:-100%;width:100%}.tab-content>.active{visibility:visible}div.csl-entry{clear:both}.hanging-indent div.csl-entry{margin-left:2em;text-indent:-2em}div.csl-left-margin{min-width:2em;float:left}div.csl-right-inline{margin-left:2em;padding-left:1em}div.csl-indent{margin-left:2em}pre,pre code{word-wrap:normal}code{overflow-wrap:break-word}.hasCopyButton{position:relative}.btn-copy-ex{position:absolute;right:5px;top:5px;visibility:hidden}.hasCopyButton:hover button.btn-copy-ex{visibility:visible}pre{padding:1rem 0.5rem}@media (max-width: 575.98px){div>div>pre{margin-left:calc(var(--bs-gutter-x) * -.5);margin-right:calc(var(--bs-gutter-x) * -.5);border-radius:0;padding-left:1rem;padding-right:1rem}.btn-copy-ex{right:calc(var(--bs-gutter-x) * -.5 + 5px)}}code a:any-link{color:inherit;text-decoration-color:#707782}pre code{padding:0;background:transparent}pre code .error,pre code .warning{font-weight:bolder}pre .img img,pre .r-plt img{margin:5px 0;background-color:#fff}@media print{code a:link:after,code a:visited:after{content:""}}a.sourceLine:hover{text-decoration:none}mark,.mark{background:linear-gradient(-100deg, rgba(3,199,232,0.2), rgba(3,199,232,0.7) 95%, rgba(3,199,232,0.1))}.algolia-autocomplete .aa-hint{color:#1D1F21}.algolia-autocomplete .aa-dropdown-menu{width:Max(100%, 20rem);background-color:#fff;border:1px solid var(--bs-border-color);margin-top:2px;max-height:50vh;overflow-y:auto}.algolia-autocomplete .aa-dropdown-menu .aa-suggestion{cursor:pointer;padding:5px 4px;border-bottom:1px #e9ecef solid;font-size:0.9rem;color:#1D1F21}.search-details{font-size:0.9rem;color:#007bc2;display:inline;font-weight:bolder}.algolia-autocomplete .aa-dropdown-menu .aa-suggestion.aa-cursor{background-color:#e6f2f9}pre{background-color:#f1f3f5}pre code{color:#003B4F}pre code span.al{color:#AD0000}pre code span.an{color:#5E5E5E}pre code span.at{color:#657422}pre code span.bn{color:#AD0000}pre code span.cf{color:#003B4F}pre code span.ch{color:#20794D}pre code span.cn{color:#8f5902}pre code span.co{color:#5E5E5E}pre code span.cv{color:#5E5E5E;font-style:italic}pre code span.do{color:#5E5E5E;font-style:italic}pre code span.dt{color:#AD0000}pre code span.dv{color:#AD0000}pre code span.er{color:#AD0000}pre code span.fl{color:#AD0000}pre code span.fu{color:#4758AB}pre code span.im{color:#00769E}pre code span.in{color:#5E5E5E}pre code span.kw{color:#003B4F}pre code span.op{color:#5E5E5E}pre code span.ot{color:#003B4F}pre code span.pp{color:#AD0000}pre code span.sc{color:#5E5E5E}pre code span.ss{color:#20794D}pre code span.st{color:#20794D}pre code span.va{color:#111111}pre code span.vs{color:#20794D}pre code span.wa{color:#5E5E5E;font-style:italic}
diff --git a/docs/deps/bootstrap-5.3.1/font.css b/docs/deps/bootstrap-5.3.1/font.css
new file mode 100644
index 0000000..fa85d55
--- /dev/null
+++ b/docs/deps/bootstrap-5.3.1/font.css
@@ -0,0 +1,1452 @@
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvZlMIXxw.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvQlMIXxw.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvYlMIXxw.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvXlMIXxw.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvblMIXxw.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvalMIXxw.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvUlMI.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvZlMIXxw.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvQlMIXxw.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvYlMIXxw.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvXlMIXxw.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvblMIXxw.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvalMIXxw.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvUlMI.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlMOvWjMY.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlOevWjMY.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlMevWjMY.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlPuvWjMY.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlMuvWjMY.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlM-vWjMY.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlPevW.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlMOvWjMY.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlOevWjMY.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlMevWjMY.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlPuvWjMY.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlMuvWjMY.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlM-vWjMY.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_SiYsKILxRpg3hIP6sJ7fM7PqlPevW.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
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-<script src="deps/search-1.0.0/mark.min.js"></script>
diff --git a/docs/index.html b/docs/index.html
index f31ff68..e440e24 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -5,51 +5,57 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<meta name="description" content="Using single cell genotype data, the cells are annotated and analysed.">
 <title>Single cell Genotyping Using RNA Data • sigurd</title>
 <script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
-<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
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-<meta name="description" content="Using single cell genotype data, the cells are annotated and analysed.">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Single cell Genotyping Using RNA Data">
 <meta property="og:description" content="Using single cell genotype data, the cells are annotated and analysed.">
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
 </head>
 <body>
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+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
-
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
-
+    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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       <ul class="navbar-nav me-auto">
-<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+<li class="nav-item">
+  <a class="nav-link" href="reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
-<li><a class="dropdown-item" href="articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
-  </ul>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
 </li>
       </ul>
-<ul class="navbar-nav">
-<li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
-</form></li>
-      </ul>
-</div>
+<form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
+</form>
 
+      <ul class="navbar-nav"></ul>
+</div>
 
+    
   </div>
 </nav><div class="container template-home">
 <div class="row">
@@ -140,19 +146,21 @@ <h2 data-toc-skip>Developers</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p>
+<p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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 </div>
 
+  
 
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 </html>
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index 1a99c65..5fccd9c 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -30,10 +30,10 @@
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-bs-original-title');
-    element.setAttribute('data-bs-original-title', msg);
+    var tooltipOriginalTitle=element.getAttribute('data-original-title');
+    element.setAttribute('data-original-title', msg);
     $(element).tooltip('show');
-    element.setAttribute('data-bs-original-title', tooltipOriginalTitle);
+    element.setAttribute('data-original-title', tooltipOriginalTitle);
   }
 
   if(ClipboardJS.isSupported()) {
@@ -60,7 +60,7 @@
         e.clearSelection();
       });
 
-      clipboard.on('error', function(e) {
+      clipboard.on('error', function() {
         changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
       });
 
@@ -153,10 +153,4 @@ async function searchFuse(query, callback) {
   });
 })(window.jQuery || window.$)
 
-document.addEventListener('keydown', function(event) {
-  // Check if the pressed key is '/'
-  if (event.key === '/') {
-    event.preventDefault();  // Prevent any default action associated with the '/' key
-    document.getElementById('search-input').focus();  // Set focus to the search input
-  }
-});
+
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 6fe1a7d..34cfa00 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,12 +1,13 @@
 pandoc: 2.0.6
-pkgdown: 2.1.1
+pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   BoneMarrow_SIGURD: BoneMarrow_SIGURD.html
   MPN_SIGURD: MPN_SIGURD.html
   SW_CellMixture_SIGURD: SW_CellMixture_SIGURD.html
   TenX_CellMixture_SIGURD: TenX_CellMixture_SIGURD.html
-last_built: 2024-10-06T14:08Z
+last_built: 2024-10-07T07:41Z
 urls:
   reference: https://costalab.github.io/sigurd/reference
   article: https://costalab.github.io/sigurd/articles
+
diff --git a/docs/reference/AllelFrequencyFoldChange.html b/docs/reference/AllelFrequencyFoldChange.html
index c368dff..9c8fc2c 100644
--- a/docs/reference/AllelFrequencyFoldChange.html
+++ b/docs/reference/AllelFrequencyFoldChange.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>AllelFrequencyFoldChange — AllelFrequencyFoldChange • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="AllelFrequencyFoldChange — AllelFrequencyFoldChange"><meta name="description" content="Check if a cell is supported by a set of variants."><meta property="og:description" content="Check if a cell is supported by a set of variants."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Check if a cell is supported by a set of variants."><title>AllelFrequencyFoldChange — AllelFrequencyFoldChange • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="AllelFrequencyFoldChange — AllelFrequencyFoldChange"><meta property="og:description" content="Check if a cell is supported by a set of variants."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
-
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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+    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>AllelFrequencyFoldChange</h1>
-
+      <img src="" class="logo" alt=""><h1>AllelFrequencyFoldChange</h1>
+      
       <div class="d-none name"><code>AllelFrequencyFoldChange.Rd</code></div>
     </div>
 
@@ -61,70 +68,68 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-voi">VOI<a class="anchor" aria-label="anchor" href="#arg-voi"></a></dt>
+<dt>VOI</dt>
 <dd><p>The variants variants to be analyzed. If NULL all are used.</p></dd>
 
 
-<dt id="arg-group-of-interest">group_of_interest<a class="anchor" aria-label="anchor" href="#arg-group-of-interest"></a></dt>
+<dt>group_of_interest</dt>
 <dd><p>The column data that divides the cells.</p></dd>
 
 
-<dt id="arg-group-">group1<a class="anchor" aria-label="anchor" href="#arg-group-"></a></dt>
+<dt>group1</dt>
 <dd><p>The first group.</p></dd>
 
 
-<dt id="arg-group-">group2<a class="anchor" aria-label="anchor" href="#arg-group-"></a></dt>
+<dt>group2</dt>
 <dd><p>The second group.</p></dd>
 
 
-<dt id="arg-maximum-foldchange">maximum_foldchange<a class="anchor" aria-label="anchor" href="#arg-maximum-foldchange"></a></dt>
+<dt>maximum_foldchange</dt>
 <dd><p>Maximum fold change.</p></dd>
 
 
-<dt id="arg-minimum-foldchange">minimum_foldchange<a class="anchor" aria-label="anchor" href="#arg-minimum-foldchange"></a></dt>
+<dt>minimum_foldchange</dt>
 <dd><p>Minimum fold change.</p></dd>
 
 
-<dt id="arg-minimum-coverage">minimum_coverage<a class="anchor" aria-label="anchor" href="#arg-minimum-coverage"></a></dt>
+<dt>minimum_coverage</dt>
 <dd><p>Minimum coverage for a variant.</p></dd>
 
 
-<dt id="arg-minimum-allele-freq">minimum_allele_freq<a class="anchor" aria-label="anchor" href="#arg-minimum-allele-freq"></a></dt>
+<dt>minimum_allele_freq</dt>
 <dd><p>Minimum allele frequency in both groups.</p></dd>
 
 
-<dt id="arg-maximum-allele-freq">maximum_allele_freq<a class="anchor" aria-label="anchor" href="#arg-maximum-allele-freq"></a></dt>
+<dt>maximum_allele_freq</dt>
 <dd><p>Maximum allele frequency in both groups.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+  
 
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diff --git a/docs/reference/AmpliconSupplementing.html b/docs/reference/AmpliconSupplementing.html
index a51a679..23dda39 100644
--- a/docs/reference/AmpliconSupplementing.html
+++ b/docs/reference/AmpliconSupplementing.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing"><meta name="description" content="We replace the values from an scRNAseq experiment with values we have from an amplicon experiment."><meta property="og:description" content="We replace the values from an scRNAseq experiment with values we have from an amplicon experiment."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We replace the values from an scRNAseq experiment with values we have from an amplicon experiment."><title>Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing"><meta property="og:description" content="We replace the values from an scRNAseq experiment with values we have from an amplicon experiment."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
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+    
 
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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+    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>Supplementing scRNAseq values with Amplicon values</h1>
-
+      <img src="" class="logo" alt=""><h1>Supplementing scRNAseq values with Amplicon values</h1>
+      
       <div class="d-none name"><code>AmpliconSupplementing.Rd</code></div>
     </div>
 
@@ -49,38 +56,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-scrnaseq">scRNAseq<a class="anchor" aria-label="anchor" href="#arg-scrnaseq"></a></dt>
+    <dl><dt>scRNAseq</dt>
 <dd><p>The SummarizedExperiment object containing the scRNAseq data.</p></dd>
 
 
-<dt id="arg-amplicon">amplicon<a class="anchor" aria-label="anchor" href="#arg-amplicon"></a></dt>
+<dt>amplicon</dt>
 <dd><p>The SummarizedExperiment object containing the amplicon data.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
-
+  
 
   </body></html>
 
diff --git a/docs/reference/CalculateAlleleFrequency.html b/docs/reference/CalculateAlleleFrequency.html
index 01fe794..aa249f9 100644
--- a/docs/reference/CalculateAlleleFrequency.html
+++ b/docs/reference/CalculateAlleleFrequency.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculating the Minor Allele Frequency. — CalculateAlleleFrequency • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculating the Minor Allele Frequency. — CalculateAlleleFrequency"><meta name="description" content="We calculate the MAF from a reference reads matrix and an alternative reads matrix.
-This function is intended to be used with the mitochondrial genome and not with other somatic mutations."><meta property="og:description" content="We calculate the MAF from a reference reads matrix and an alternative reads matrix.
-This function is intended to be used with the mitochondrial genome and not with other somatic mutations."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We calculate the MAF from a reference reads matrix and an alternative reads matrix.
+This function is intended to be used with the mitochondrial genome and not with other somatic mutations."><title>Calculating the Minor Allele Frequency. — CalculateAlleleFrequency • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculating the Minor Allele Frequency. — CalculateAlleleFrequency"><meta property="og:description" content="We calculate the MAF from a reference reads matrix and an alternative reads matrix.
+This function is intended to be used with the mitochondrial genome and not with other somatic mutations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
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 </nav><div class="container template-reference-topic">
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   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>Calculating the Minor Allele Frequency.</h1>
-
+      <img src="" class="logo" alt=""><h1>Calculating the Minor Allele Frequency.</h1>
+      
       <div class="d-none name"><code>CalculateAlleleFrequency.Rd</code></div>
     </div>
 
@@ -52,38 +59,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-reference-reads">reference_reads<a class="anchor" aria-label="anchor" href="#arg-reference-reads"></a></dt>
+    <dl><dt>reference_reads</dt>
 <dd><p>Reference reads matrix.</p></dd>
 
 
-<dt id="arg-alternative-reads">alternative_reads<a class="anchor" aria-label="anchor" href="#arg-alternative-reads"></a></dt>
+<dt>alternative_reads</dt>
 <dd><p>List of matrices for the alternative reads.</p></dd>
 
 
-<dt id="arg-pseudo-count">pseudo_count<a class="anchor" aria-label="anchor" href="#arg-pseudo-count"></a></dt>
+<dt>pseudo_count</dt>
 <dd><p>= What is the pseudo count you want to add to the reference_reads matrix. Default = 0</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+  
 
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+  
 
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diff --git a/docs/reference/CalculateAltReads.html b/docs/reference/CalculateAltReads.html
index dcca579..9871d71 100644
--- a/docs/reference/CalculateAltReads.html
+++ b/docs/reference/CalculateAltReads.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>CalculateAltReads — CalculateAltReads • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateAltReads — CalculateAltReads"><meta name="description" content="We calculate the number of reads covering a variant using forward and reverse reads."><meta property="og:description" content="We calculate the number of reads covering a variant using forward and reverse reads."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We calculate the number of reads covering a variant using forward and reverse reads."><title>CalculateAltReads — CalculateAltReads • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateAltReads — CalculateAltReads"><meta property="og:description" content="We calculate the number of reads covering a variant using forward and reverse reads."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
-
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>CalculateAltReads</h1>
-
+      <img src="" class="logo" alt=""><h1>CalculateAltReads</h1>
+      
       <div class="d-none name"><code>CalculateAltReads.Rd</code></div>
     </div>
 
@@ -49,34 +56,32 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>List of matrices for the alternative reads.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
-
+  
 
   </body></html>
 
diff --git a/docs/reference/CalculateConsensus.html b/docs/reference/CalculateConsensus.html
index f748c4f..6b4ffa3 100644
--- a/docs/reference/CalculateConsensus.html
+++ b/docs/reference/CalculateConsensus.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>CalculateConsensus — CalculateConsensus • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateConsensus — CalculateConsensus"><meta name="description" content="We calculate the consensus information from the MAEGATK results.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We calculate the consensus information from the MAEGATK results.
 We set cells that have only alternative reads to 2 (Alternative).
 We set cells that have only reference reads to 1 (Reference).
 We set cells that have a mixture of alternative and reference reads to 3 (Both).
@@ -9,7 +9,7 @@
 For example:
 A cell has at position 3: 0 A reads, 53 T reads, 63 C reads, 148 T reads.
 For the variant chrM_3_T_A, the cell would have 53 reference reads, but also reads for other variants at this position.
-To make sure that there is no confusion, the cell is set to NoCall."><meta property="og:description" content="We calculate the consensus information from the MAEGATK results.
+To make sure that there is no confusion, the cell is set to NoCall."><title>CalculateConsensus — CalculateConsensus • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateConsensus — CalculateConsensus"><meta property="og:description" content="We calculate the consensus information from the MAEGATK results.
 We set cells that have only alternative reads to 2 (Alternative).
 We set cells that have only reference reads to 1 (Reference).
 We set cells that have a mixture of alternative and reference reads to 3 (Both).
@@ -19,42 +19,49 @@
 For example:
 A cell has at position 3: 0 A reads, 53 T reads, 63 C reads, 148 T reads.
 For the variant chrM_3_T_A, the cell would have 53 reference reads, but also reads for other variants at this position.
-To make sure that there is no confusion, the cell is set to NoCall."></head><body>
+To make sure that there is no confusion, the cell is set to NoCall."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
-
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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+    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>CalculateConsensus</h1>
-
+      <img src="" class="logo" alt=""><h1>CalculateConsensus</h1>
+      
       <div class="d-none name"><code>CalculateConsensus.Rd</code></div>
     </div>
 
@@ -79,38 +86,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>The chromosome name used as a prefix.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = FALSE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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diff --git a/docs/reference/CalculateCorrelationPValue.html b/docs/reference/CalculateCorrelationPValue.html
index 168b04f..e253540 100644
--- a/docs/reference/CalculateCorrelationPValue.html
+++ b/docs/reference/CalculateCorrelationPValue.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Correlating the SNVs — CalculateCorrelationPValue • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Correlating the SNVs — CalculateCorrelationPValue"><meta name="description" content="We perform the correlation of SNVs and calculate the P values."><meta property="og:description" content="We perform the correlation of SNVs and calculate the P values."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We perform the correlation of SNVs and calculate the P values."><title>Correlating the SNVs — CalculateCorrelationPValue • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Correlating the SNVs — CalculateCorrelationPValue"><meta property="og:description" content="We perform the correlation of SNVs and calculate the P values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+    
 
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     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>Correlating the SNVs</h1>
-
+      <img src="" class="logo" alt=""><h1>Correlating the SNVs</h1>
+      
       <div class="d-none name"><code>CalculateCorrelationPValue.Rd</code></div>
     </div>
 
@@ -54,42 +61,40 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-variant-values">variant_values<a class="anchor" aria-label="anchor" href="#arg-variant-values"></a></dt>
+    <dl><dt>variant_values</dt>
 <dd><p>The fraction values you are analysing. A vector.</p></dd>
 
 
-<dt id="arg-other-mutation">other_mutation<a class="anchor" aria-label="anchor" href="#arg-other-mutation"></a></dt>
+<dt>other_mutation</dt>
 <dd><p>All other variants you have. A vector of variant names.</p></dd>
 
 
-<dt id="arg-all-variants-list">all_variants_list<a class="anchor" aria-label="anchor" href="#arg-all-variants-list"></a></dt>
+<dt>all_variants_list</dt>
 <dd><p>List of fraction values for all the variants you want to compare your variant with.</p></dd>
 
 
-<dt id="arg-min-intersecting-cells">min_intersecting_cells<a class="anchor" aria-label="anchor" href="#arg-min-intersecting-cells"></a></dt>
+<dt>min_intersecting_cells</dt>
 <dd><p>Minimum number of intersecting cells. Correlations with less than this will not be performed.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
-
+  
 
   </body></html>
 
diff --git a/docs/reference/CalculateCoverage.html b/docs/reference/CalculateCoverage.html
index f9a0553..ad5c14a 100644
--- a/docs/reference/CalculateCoverage.html
+++ b/docs/reference/CalculateCoverage.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>CalculateCoverage — CalculateCoverage • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateCoverage — CalculateCoverage"><meta name="description" content="We calculate the coverage information per variant from the MAEGATK results."><meta property="og:description" content="We calculate the coverage information per variant from the MAEGATK results."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We calculate the coverage information per variant from the MAEGATK results."><title>CalculateCoverage — CalculateCoverage • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateCoverage — CalculateCoverage"><meta property="og:description" content="We calculate the coverage information per variant from the MAEGATK results."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
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+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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+    
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   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>CalculateCoverage</h1>
-
+      <img src="" class="logo" alt=""><h1>CalculateCoverage</h1>
+      
       <div class="d-none name"><code>CalculateCoverage.Rd</code></div>
     </div>
 
@@ -49,34 +56,32 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>List of matrices for the alternative reads.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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diff --git a/docs/reference/CalculateFisherTestPValue.html b/docs/reference/CalculateFisherTestPValue.html
index 9156172..0d9a3a1 100644
--- a/docs/reference/CalculateFisherTestPValue.html
+++ b/docs/reference/CalculateFisherTestPValue.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>CalculateFisherTestPValue — CalculateFisherTestPValue • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateFisherTestPValue — CalculateFisherTestPValue"><meta name="description" content="We perform the Fisher Test of SNVs and calculate the P values."><meta property="og:description" content="We perform the Fisher Test of SNVs and calculate the P values."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We perform the Fisher Test of SNVs and calculate the P values."><title>CalculateFisherTestPValue — CalculateFisherTestPValue • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateFisherTestPValue — CalculateFisherTestPValue"><meta property="og:description" content="We perform the Fisher Test of SNVs and calculate the P values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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-
-      <h1>CalculateFisherTestPValue</h1>
-
+      <img src="" class="logo" alt=""><h1>CalculateFisherTestPValue</h1>
+      
       <div class="d-none name"><code>CalculateFisherTestPValue.Rd</code></div>
     </div>
 
@@ -54,42 +61,40 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-variant-values">variant_values<a class="anchor" aria-label="anchor" href="#arg-variant-values"></a></dt>
+    <dl><dt>variant_values</dt>
 <dd><p>The fraction values you are analysing. A vector.</p></dd>
 
 
-<dt id="arg-other-mutation">other_mutation<a class="anchor" aria-label="anchor" href="#arg-other-mutation"></a></dt>
+<dt>other_mutation</dt>
 <dd><p>All other variants you have. A vector of variant names.</p></dd>
 
 
-<dt id="arg-all-variants-list">all_variants_list<a class="anchor" aria-label="anchor" href="#arg-all-variants-list"></a></dt>
+<dt>all_variants_list</dt>
 <dd><p>List of fraction values for all the variants you want to compare your variant with.</p></dd>
 
 
-<dt id="arg-min-intersecting-cells">min_intersecting_cells<a class="anchor" aria-label="anchor" href="#arg-min-intersecting-cells"></a></dt>
+<dt>min_intersecting_cells</dt>
 <dd><p>Minimum number of intersecting cells. Correlations with less than this will not be performed.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/CalculateQuality.html b/docs/reference/CalculateQuality.html
index ab28aa2..5dc187c 100644
--- a/docs/reference/CalculateQuality.html
+++ b/docs/reference/CalculateQuality.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>CalculateQuality — CalculateQuality • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateQuality — CalculateQuality"><meta name="description" content="We calculate the quality per variant."><meta property="og:description" content="We calculate the quality per variant."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We calculate the quality per variant."><title>CalculateQuality — CalculateQuality • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateQuality — CalculateQuality"><meta property="og:description" content="We calculate the quality per variant."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+<![endif]--></head><body>
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+    
 
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+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>CalculateQuality</h1>
-
+      <img src="" class="logo" alt=""><h1>CalculateQuality</h1>
+      
       <div class="d-none name"><code>CalculateQuality.Rd</code></div>
     </div>
 
@@ -49,38 +56,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-variants">variants<a class="anchor" aria-label="anchor" href="#arg-variants"></a></dt>
+<dt>variants</dt>
 <dd><p>The variants you want to get the quality for.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>List of matrices for the alternative reads.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
-
+  
 
   </body></html>
 
diff --git a/docs/reference/CalculateRefReads.html b/docs/reference/CalculateRefReads.html
index c958c2b..e5bd791 100644
--- a/docs/reference/CalculateRefReads.html
+++ b/docs/reference/CalculateRefReads.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
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     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
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+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
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-      <h1>CalculateRefReads</h1>
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+      <img src="" class="logo" alt=""><h1>CalculateRefReads</h1>
+      
       <div class="d-none name"><code>CalculateRefReads.Rd</code></div>
     </div>
 
@@ -49,34 +56,32 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>List of matrices for the reference reads.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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diff --git a/docs/reference/CalculateStrandCorrelation.html b/docs/reference/CalculateStrandCorrelation.html
index 50d86df..93146f3 100644
--- a/docs/reference/CalculateStrandCorrelation.html
+++ b/docs/reference/CalculateStrandCorrelation.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>CalculateStrandCorrelation — CalculateStrandCorrelation • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateStrandCorrelation — CalculateStrandCorrelation"><meta name="description" content="We calculate the correlation between the amount of forward and reverse reads per variant."><meta property="og:description" content="We calculate the correlation between the amount of forward and reverse reads per variant."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We calculate the correlation between the amount of forward and reverse reads per variant."><title>CalculateStrandCorrelation — CalculateStrandCorrelation • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CalculateStrandCorrelation — CalculateStrandCorrelation"><meta property="og:description" content="We calculate the correlation between the amount of forward and reverse reads per variant."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
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+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
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-
-      <h1>CalculateStrandCorrelation</h1>
-
+      <img src="" class="logo" alt=""><h1>CalculateStrandCorrelation</h1>
+      
       <div class="d-none name"><code>CalculateStrandCorrelation.Rd</code></div>
     </div>
 
@@ -49,34 +56,32 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>List of matrices for the alternative reads.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/CallSupport.html b/docs/reference/CallSupport.html
index 7194b21..6b376da 100644
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@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>CallSupport — CallSupport • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CallSupport — CallSupport"><meta name="description" content="Check if a cell is supported by a set of variants."><meta property="og:description" content="Check if a cell is supported by a set of variants."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Check if a cell is supported by a set of variants."><title>CallSupport — CallSupport • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CallSupport — CallSupport"><meta property="og:description" content="Check if a cell is supported by a set of variants."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
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-
-      <h1>CallSupport</h1>
-
+      <img src="" class="logo" alt=""><h1>CallSupport</h1>
+      
       <div class="d-none name"><code>CallSupport.Rd</code></div>
     </div>
 
@@ -60,70 +67,68 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-voi-group-">VOI_group1<a class="anchor" aria-label="anchor" href="#arg-voi-group-"></a></dt>
+<dt>VOI_group1</dt>
 <dd><p>The variants supporting the first group.</p></dd>
 
 
-<dt id="arg-voi-group-">VOI_group2<a class="anchor" aria-label="anchor" href="#arg-voi-group-"></a></dt>
+<dt>VOI_group2</dt>
 <dd><p>The variants supporting the second group.</p></dd>
 
 
-<dt id="arg-group-name">group1_name<a class="anchor" aria-label="anchor" href="#arg-group-name"></a></dt>
+<dt>group1_name</dt>
 <dd><p>The name used for the first group.</p></dd>
 
 
-<dt id="arg-group-name">group2_name<a class="anchor" aria-label="anchor" href="#arg-group-name"></a></dt>
+<dt>group2_name</dt>
 <dd><p>The name used for the second group.</p></dd>
 
 
-<dt id="arg-min-mutated-reads">min_mutated_reads<a class="anchor" aria-label="anchor" href="#arg-min-mutated-reads"></a></dt>
+<dt>min_mutated_reads</dt>
 <dd><p>The minimum number of mutated reads in a cell supporting a group.</p></dd>
 
 
-<dt id="arg-min-reads">min_reads<a class="anchor" aria-label="anchor" href="#arg-min-reads"></a></dt>
+<dt>min_reads</dt>
 <dd><p>Minimum number of reads per cell for a classification.</p></dd>
 
 
-<dt id="arg-group-factor">group_factor<a class="anchor" aria-label="anchor" href="#arg-group-factor"></a></dt>
+<dt>group_factor</dt>
 <dd><p>How much higher has the mean allele frequency to be in group 1 when compared to group 2 and vice versa? Can be a vector of length 2.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 
-<dt id="arg-return-nonsupport">return_nonsupport<a class="anchor" aria-label="anchor" href="#arg-return-nonsupport"></a></dt>
+<dt>return_nonsupport</dt>
 <dd><p>Should nonsupporting cells be return too? Default FALSE.</p></dd>
 
 
-<dt id="arg-group-of-interest">group_of_interest<a class="anchor" aria-label="anchor" href="#arg-group-of-interest"></a></dt>
+<dt>group_of_interest</dt>
 <dd><p>The column data that divides the cells.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/ClonalDefinition.html b/docs/reference/ClonalDefinition.html
index 688a66c..5d23b6e 100644
--- a/docs/reference/ClonalDefinition.html
+++ b/docs/reference/ClonalDefinition.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Defining clones. — ClonalDefinition • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Defining clones. — ClonalDefinition"><meta name="description" content="This function defines clones using a combination of variants supplied. Each set of variants can be and should be paired with a identity, like sample or cell type. The clones are then only determined in respect to this group. If this information is not provided, the clones are determined for all cells present."><meta property="og:description" content="This function defines clones using a combination of variants supplied. Each set of variants can be and should be paired with a identity, like sample or cell type. The clones are then only determined in respect to this group. If this information is not provided, the clones are determined for all cells present."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function defines clones using a combination of variants supplied. Each set of variants can be and should be paired with a identity, like sample or cell type. The clones are then only determined in respect to this group. If this information is not provided, the clones are determined for all cells present."><title>Defining clones. — ClonalDefinition • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Defining clones. — ClonalDefinition"><meta property="og:description" content="This function defines clones using a combination of variants supplied. Each set of variants can be and should be paired with a identity, like sample or cell type. The clones are then only determined in respect to this group. If this information is not provided, the clones are determined for all cells present."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+    
 
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+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
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 </nav><div class="container template-reference-topic">
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-
-      <h1>Defining clones.</h1>
-
+      <img src="" class="logo" alt=""><h1>Defining clones.</h1>
+      
       <div class="d-none name"><code>ClonalDefinition.Rd</code></div>
     </div>
 
@@ -58,58 +65,56 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">se<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>se</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-variants-ls">variants_ls<a class="anchor" aria-label="anchor" href="#arg-variants-ls"></a></dt>
+<dt>variants_ls</dt>
 <dd><p>List of variants for clonal definition</p></dd>
 
 
-<dt id="arg-grouping">grouping<a class="anchor" aria-label="anchor" href="#arg-grouping"></a></dt>
+<dt>grouping</dt>
 <dd><p>The meta data    column used to split the cells into groups. Default = NULL</p></dd>
 
 
-<dt id="arg-identities">identities<a class="anchor" aria-label="anchor" href="#arg-identities"></a></dt>
+<dt>identities</dt>
 <dd><p>Vector of groups, like samples.</p></dd>
 
 
-<dt id="arg-explicit">explicit<a class="anchor" aria-label="anchor" href="#arg-explicit"></a></dt>
+<dt>explicit</dt>
 <dd><p>Do you want to specify the variants forming a clone? Then the variant_ls needs to be a list of variants that each define a clone. One variant per group.</p></dd>
 
 
-<dt id="arg-explicit-not">explicit_not<a class="anchor" aria-label="anchor" href="#arg-explicit-not"></a></dt>
+<dt>explicit_not</dt>
 <dd><p>Do you want to specify a set of variants that the cell may not have? One set per group.</p></dd>
 
 
-<dt id="arg-explicit-min-vaf">explicit_min_vaf<a class="anchor" aria-label="anchor" href="#arg-explicit-min-vaf"></a></dt>
+<dt>explicit_min_vaf</dt>
 <dd><p>Minimum VAF for a cell to be considered positive.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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diff --git a/docs/reference/ClonalDiversity.html b/docs/reference/ClonalDiversity.html
index dbe0349..613a86e 100644
--- a/docs/reference/ClonalDiversity.html
+++ b/docs/reference/ClonalDiversity.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Determining the clonal diversity. — ClonalDiversity • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Determining the clonal diversity. — ClonalDiversity"><meta name="description" content="This function determines the clonal diversity. The clones are defined using the function ClonalDefinition. It is not required to use clones, but any column in the column data of the object can be used."><meta property="og:description" content="This function determines the clonal diversity. The clones are defined using the function ClonalDefinition. It is not required to use clones, but any column in the column data of the object can be used."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function determines the clonal diversity. The clones are defined using the function ClonalDefinition. It is not required to use clones, but any column in the column data of the object can be used."><title>Determining the clonal diversity. — ClonalDiversity • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Determining the clonal diversity. — ClonalDiversity"><meta property="og:description" content="This function determines the clonal diversity. The clones are defined using the function ClonalDefinition. It is not required to use clones, but any column in the column data of the object can be used."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
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     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>Determining the clonal diversity.</h1>
-
+      <img src="" class="logo" alt=""><h1>Determining the clonal diversity.</h1>
+      
       <div class="d-none name"><code>ClonalDiversity.Rd</code></div>
     </div>
 
@@ -56,50 +63,48 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">se<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>se</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-grouping">grouping<a class="anchor" aria-label="anchor" href="#arg-grouping"></a></dt>
+<dt>grouping</dt>
 <dd><p>The meta data    column used.</p></dd>
 
 
-<dt id="arg-cells">cells<a class="anchor" aria-label="anchor" href="#arg-cells"></a></dt>
+<dt>cells</dt>
 <dd><p>Which cells should be used? NULL uses all cells.</p></dd>
 
 
-<dt id="arg-diversity-measure">diversity_measure<a class="anchor" aria-label="anchor" href="#arg-diversity-measure"></a></dt>
+<dt>diversity_measure</dt>
 <dd><p>What diversity measure should be calculated? Can be EffectiveSpecies, shannon, simpson, invsimpson</p></dd>
 
 
-<dt id="arg-base">base<a class="anchor" aria-label="anchor" href="#arg-base"></a></dt>
+<dt>base</dt>
 <dd><p>The base for the diversity</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
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+  
 
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diff --git a/docs/reference/CombineSEobjects.html b/docs/reference/CombineSEobjects.html
index 8499b6b..75a888c 100644
--- a/docs/reference/CombineSEobjects.html
+++ b/docs/reference/CombineSEobjects.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>CombineSEobjects — CombineSEobjects • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CombineSEobjects — CombineSEobjects"><meta name="description" content="We combine two SummarizedExperiment objects. This is originally intended to add the mitochondrial genotyping information to the somatic genotyping information.
-The function can combine any two objects and it is not requried to be from two different genotyping results."><meta property="og:description" content="We combine two SummarizedExperiment objects. This is originally intended to add the mitochondrial genotyping information to the somatic genotyping information.
-The function can combine any two objects and it is not requried to be from two different genotyping results."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We combine two SummarizedExperiment objects. This is originally intended to add the mitochondrial genotyping information to the somatic genotyping information.
+The function can combine any two objects and it is not requried to be from two different genotyping results."><title>CombineSEobjects — CombineSEobjects • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CombineSEobjects — CombineSEobjects"><meta property="og:description" content="We combine two SummarizedExperiment objects. This is originally intended to add the mitochondrial genotyping information to the somatic genotyping information.
+The function can combine any two objects and it is not requried to be from two different genotyping results."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+    
 
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+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>CombineSEobjects</h1>
-
+      <img src="" class="logo" alt=""><h1>CombineSEobjects</h1>
+      
       <div class="d-none name"><code>CombineSEobjects.Rd</code></div>
     </div>
 
@@ -52,38 +59,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se-">se_1<a class="anchor" aria-label="anchor" href="#arg-se-"></a></dt>
+    <dl><dt>se_1</dt>
 <dd><p>SummarizedExperiment object 1.</p></dd>
 
 
-<dt id="arg-se-">se_2<a class="anchor" aria-label="anchor" href="#arg-se-"></a></dt>
+<dt>se_2</dt>
 <dd><p>SummarizedExperiment object 2.</p></dd>
 
 
-<dt id="arg-suffixes">suffixes<a class="anchor" aria-label="anchor" href="#arg-suffixes"></a></dt>
+<dt>suffixes</dt>
 <dd><p>The suffixes you want to add to the meta data.frame.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+  
 
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diff --git a/docs/reference/Enrichment_FisherTest.html b/docs/reference/Enrichment_FisherTest.html
index fc1721b..3ba9990 100644
--- a/docs/reference/Enrichment_FisherTest.html
+++ b/docs/reference/Enrichment_FisherTest.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Enrichment_FisherTest — Enrichment_FisherTest • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Enrichment_FisherTest — Enrichment_FisherTest"><meta name="description" content="This function performs the Fisher test. The specified variant is"><meta property="og:description" content="This function performs the Fisher test. The specified variant is"></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function performs the Fisher test. The specified variant is"><title>Enrichment_FisherTest — Enrichment_FisherTest • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Enrichment_FisherTest — Enrichment_FisherTest"><meta property="og:description" content="This function performs the Fisher test. The specified variant is"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>Enrichment_FisherTest</h1>
-
+      <img src="" class="logo" alt=""><h1>Enrichment_FisherTest</h1>
+      
       <div class="d-none name"><code>Enrichment_FisherTest.Rd</code></div>
     </div>
 
@@ -56,50 +63,48 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">se<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>se</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-variant">variant<a class="anchor" aria-label="anchor" href="#arg-variant"></a></dt>
+<dt>variant</dt>
 <dd><p>The variant to be analysed. The values for this variant are retrieved from the consensus assay.</p></dd>
 
 
-<dt id="arg-use-nocall">use_nocall<a class="anchor" aria-label="anchor" href="#arg-use-nocall"></a></dt>
+<dt>use_nocall</dt>
 <dd><p>Should the NoCall values be used? Then the non genotyped cells would be a separate group in addition to Alt and Ref. If FALSE, the NoCalls are removed. Default = FALSE</p></dd>
 
 
-<dt id="arg-both-as-alt">both_as_alt<a class="anchor" aria-label="anchor" href="#arg-both-as-alt"></a></dt>
+<dt>both_as_alt</dt>
 <dd><p>Should the consensus value for heterozyguous (3 or both) be treated as homozyguous (Alt)? Default = TRUE</p></dd>
 
 
-<dt id="arg-trait">trait<a class="anchor" aria-label="anchor" href="#arg-trait"></a></dt>
+<dt>trait</dt>
 <dd><p>The trait the variant should be associated to. This can be any column from the colData of the object.</p></dd>
 
 
-<dt id="arg-trait-levels">trait_levels<a class="anchor" aria-label="anchor" href="#arg-trait-levels"></a></dt>
+<dt>trait_levels</dt>
 <dd><p>Should only trait levels be used for the comparison? For example, if Sample 1-3 are present but only 1 and 2 should be used in the comparison use trait_levels = c("Sample_1", "Sample_2"). NULL uses all levels. Default = NULL</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
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diff --git a/docs/reference/Filtering.html b/docs/reference/Filtering.html
index d024281..b2c10e2 100644
--- a/docs/reference/Filtering.html
+++ b/docs/reference/Filtering.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Filtering the loaded genotyping data. — Filtering • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Filtering the loaded genotyping data. — Filtering"><meta name="description" content="We filter a SummarizedExperiment object to exclude variants and cells."><meta property="og:description" content="We filter a SummarizedExperiment object to exclude variants and cells."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We filter a SummarizedExperiment object to exclude variants and cells."><title>Filtering the loaded genotyping data. — Filtering • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Filtering the loaded genotyping data. — Filtering"><meta property="og:description" content="We filter a SummarizedExperiment object to exclude variants and cells."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+    
 
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+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>Filtering the loaded genotyping data.</h1>
-
+      <img src="" class="logo" alt=""><h1>Filtering the loaded genotyping data.</h1>
+      
       <div class="d-none name"><code>Filtering.Rd</code></div>
     </div>
 
@@ -59,41 +66,39 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-cells-include">cells_include<a class="anchor" aria-label="anchor" href="#arg-cells-include"></a></dt>
+<dt>cells_include</dt>
 <dd><p>A vector of cell barcodes. Only these cells will be retained.</p></dd>
 
 
-<dt id="arg-cells-exclude">cells_exclude<a class="anchor" aria-label="anchor" href="#arg-cells-exclude"></a></dt>
+<dt>cells_exclude</dt>
 <dd><p>A vector of cell barcodes. These cells will be removed from the output.</p></dd>
 
 
-<dt id="arg-fraction-threshold">fraction_threshold<a class="anchor" aria-label="anchor" href="#arg-fraction-threshold"></a></dt>
+<dt>fraction_threshold</dt>
 <dd><p>Variants with an VAF below this threshold are set to 0. Numeric. Default = NULL.</p></dd>
 
 
-<dt id="arg-alts-threshold">alts_threshold<a class="anchor" aria-label="anchor" href="#arg-alts-threshold"></a></dt>
+<dt>alts_threshold</dt>
 <dd><p>Variants with a number of alt reads less than this threshold are set to 0. Numeric. Default = NULL.</p></dd>
 
 
-<dt id="arg-min-cells-per-variant">min_cells_per_variant<a class="anchor" aria-label="anchor" href="#arg-min-cells-per-variant"></a></dt>
+<dt>min_cells_per_variant</dt>
 <dd><p>In how many cells should a variant be present to be included? Numeric. Default = 2.</p></dd>
 
 
-<dt id="arg-min-variants-per-cell">min_variants_per_cell<a class="anchor" aria-label="anchor" href="#arg-min-variants-per-cell"></a></dt>
+<dt>min_variants_per_cell</dt>
 <dd><p>How many variants should be covered in a cell have to be included? Default = 1.</p></dd>
 
 
-<dt id="arg-reject-value">reject_value<a class="anchor" aria-label="anchor" href="#arg-reject-value"></a></dt>
+<dt>reject_value</dt>
 <dd><p>Should cells that fall below a threshold (fraction_threshold or alts_threshold) be treated as Reference or NoCall? Default = NoCall.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
@@ -110,30 +115,30 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># Removing all variants that are not detected in at least 2 cells.</span></span></span>
 <span class="r-in"><span>  <span class="co"># Before we remove the variants, we set fraction value of variants below 0.05 to 0.</span></span></span>
 <span class="r-in"><span>  <span class="va">se_geno</span> <span class="op">&lt;-</span> <span class="fu">Filtering</span><span class="op">(</span><span class="va">se_geno</span>, min_cells_per_variant <span class="op">=</span> <span class="fl">2</span>, fraction_threshold <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
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+  
 
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diff --git a/docs/reference/GetCellInfoPerVariant.html b/docs/reference/GetCellInfoPerVariant.html
index bba4a95..c54aea5 100644
--- a/docs/reference/GetCellInfoPerVariant.html
+++ b/docs/reference/GetCellInfoPerVariant.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>We get the variant information per cell. — GetCellInfoPerVariant • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="We get the variant information per cell. — GetCellInfoPerVariant"><meta name="description" content="We get the variant information per cell."><meta property="og:description" content="We get the variant information per cell."></head><body>
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>We get the variant information per cell.</h1>
-
+      <img src="" class="logo" alt=""><h1>We get the variant information per cell.</h1>
+      
       <div class="d-none name"><code>GetCellInfoPerVariant.Rd</code></div>
     </div>
 
@@ -49,38 +56,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">se<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>se</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-voi-ch">voi_ch<a class="anchor" aria-label="anchor" href="#arg-voi-ch"></a></dt>
+<dt>voi_ch</dt>
 <dd><p>Variants of interest.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = FALSE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
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+  
 
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diff --git a/docs/reference/GetVariantInfo.html b/docs/reference/GetVariantInfo.html
index 0c14a9d..35f88a9 100644
--- a/docs/reference/GetVariantInfo.html
+++ b/docs/reference/GetVariantInfo.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>GetVariantInfo — GetVariantInfo • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GetVariantInfo — GetVariantInfo"><meta name="description" content="We get the genotyping information for a set of variants.
-The function returns a matrix with the values from the specified assay."><meta property="og:description" content="We get the genotyping information for a set of variants.
-The function returns a matrix with the values from the specified assay."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We get the genotyping information for a set of variants.
+The function returns a matrix with the values from the specified assay."><title>GetVariantInfo — GetVariantInfo • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GetVariantInfo — GetVariantInfo"><meta property="og:description" content="We get the genotyping information for a set of variants.
+The function returns a matrix with the values from the specified assay."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>GetVariantInfo</h1>
-
+      <img src="" class="logo" alt=""><h1>GetVariantInfo</h1>
+      
       <div class="d-none name"><code>GetVariantInfo.Rd</code></div>
     </div>
 
@@ -52,42 +59,40 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-information">information<a class="anchor" aria-label="anchor" href="#arg-information"></a></dt>
+<dt>information</dt>
 <dd><p>The assay with the desired information. Default: consensus</p></dd>
 
 
-<dt id="arg-variants">variants<a class="anchor" aria-label="anchor" href="#arg-variants"></a></dt>
+<dt>variants</dt>
 <dd><p>A vector of variants.</p></dd>
 
 
-<dt id="arg-cells">cells<a class="anchor" aria-label="anchor" href="#arg-cells"></a></dt>
+<dt>cells</dt>
 <dd><p>A vector of cell IDs. On default all cells are returned. Default: NULL</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
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+  
 
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diff --git a/docs/reference/HeatmapVoi.html b/docs/reference/HeatmapVoi.html
index a9d6609..f5b1dcc 100644
--- a/docs/reference/HeatmapVoi.html
+++ b/docs/reference/HeatmapVoi.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>HeatmapVoi — HeatmapVoi • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="HeatmapVoi — HeatmapVoi"><meta name="description" content="We plot a heatmap of a set of Variants Of Interest using the Variant Allele Frequency values of a SummarizedExperiment object."><meta property="og:description" content="We plot a heatmap of a set of Variants Of Interest using the Variant Allele Frequency values of a SummarizedExperiment object."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We plot a heatmap of a set of Variants Of Interest using the Variant Allele Frequency values of a SummarizedExperiment object."><title>HeatmapVoi — HeatmapVoi • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="HeatmapVoi — HeatmapVoi"><meta property="og:description" content="We plot a heatmap of a set of Variants Of Interest using the Variant Allele Frequency values of a SummarizedExperiment object."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
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+    
 
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     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
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 <li class="nav-item dropdown">
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>HeatmapVoi</h1>
-
+      <img src="" class="logo" alt=""><h1>HeatmapVoi</h1>
+      
       <div class="d-none name"><code>HeatmapVoi.Rd</code></div>
     </div>
 
@@ -61,70 +68,68 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-voi">voi<a class="anchor" aria-label="anchor" href="#arg-voi"></a></dt>
+<dt>voi</dt>
 <dd><p>Variants Of Interest.</p></dd>
 
 
-<dt id="arg-annotation-trait">annotation_trait<a class="anchor" aria-label="anchor" href="#arg-annotation-trait"></a></dt>
+<dt>annotation_trait</dt>
 <dd><p>Cell Annotation at the bottom of the heat map.</p></dd>
 
 
-<dt id="arg-column-title">column_title<a class="anchor" aria-label="anchor" href="#arg-column-title"></a></dt>
+<dt>column_title</dt>
 <dd><p>The title of the heat map. Default = NULL</p></dd>
 
 
-<dt id="arg-minimum-coverage">minimum_coverage<a class="anchor" aria-label="anchor" href="#arg-minimum-coverage"></a></dt>
+<dt>minimum_coverage</dt>
 <dd><p>The minimum coverage per cell to be plotted.</p></dd>
 
 
-<dt id="arg-sort-cells">sort_cells<a class="anchor" aria-label="anchor" href="#arg-sort-cells"></a></dt>
+<dt>sort_cells</dt>
 <dd><p>Should the cells be sorted by ordering the cells according the the largest clones? FALSE uses default complete clustering with euclidean distance.</p></dd>
 
 
-<dt id="arg-remove-empty-cells">remove_empty_cells<a class="anchor" aria-label="anchor" href="#arg-remove-empty-cells"></a></dt>
+<dt>remove_empty_cells</dt>
 <dd><p>Should cells that have a fraction of 0 for all variants be removed? Default = FALSE</p></dd>
 
 
-<dt id="arg-minimum-allele-freq">minimum_allele_freq<a class="anchor" aria-label="anchor" href="#arg-minimum-allele-freq"></a></dt>
+<dt>minimum_allele_freq</dt>
 <dd><p>Minimum allele frequency to include a cell.</p></dd>
 
 
-<dt id="arg-cluster-variants">cluster_variants<a class="anchor" aria-label="anchor" href="#arg-cluster-variants"></a></dt>
+<dt>cluster_variants</dt>
 <dd><p>Should the variants be clustered? Default FALSE.</p></dd>
 
 
-<dt id="arg-cluster-variants-distance">cluster_variants_distance<a class="anchor" aria-label="anchor" href="#arg-cluster-variants-distance"></a></dt>
+<dt>cluster_variants_distance</dt>
 <dd><p>The distance for clustering the variants. Default euclidean.</p></dd>
 
 
-<dt id="arg-cluster-variants-method">cluster_variants_method<a class="anchor" aria-label="anchor" href="#arg-cluster-variants-method"></a></dt>
+<dt>cluster_variants_method</dt>
 <dd><p>The distance for the variant clustering. Default complete</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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+  
 
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diff --git a/docs/reference/LoadingMAEGATK_typewise.html b/docs/reference/LoadingMAEGATK_typewise.html
index b97aa8b..b55ca5a 100644
--- a/docs/reference/LoadingMAEGATK_typewise.html
+++ b/docs/reference/LoadingMAEGATK_typewise.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>LoadingMAEGATK_typewise — LoadingMAEGATK_typewise • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="LoadingMAEGATK_typewise — LoadingMAEGATK_typewise"><meta name="description" content="We load the MAEGATK output and transform it to be compatible with the VarTrix output.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We load the MAEGATK output and transform it to be compatible with the VarTrix output.
 The input file is a specifically formated csv file with all the necessary information to run the analysis.
 Note that the source column in the input file needs to be mgaetk or mgatk for this function. This is case insensitive.
 If you want to only load a single sample without the use of an input file, you have to set the following variables.
@@ -8,7 +8,7 @@
 patient
 samples_file = NULL
 
-"><meta property="og:description" content="We load the MAEGATK output and transform it to be compatible with the VarTrix output.
+"><title>LoadingMAEGATK_typewise — LoadingMAEGATK_typewise • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="LoadingMAEGATK_typewise — LoadingMAEGATK_typewise"><meta property="og:description" content="We load the MAEGATK output and transform it to be compatible with the VarTrix output.
 The input file is a specifically formated csv file with all the necessary information to run the analysis.
 Note that the source column in the input file needs to be mgaetk or mgatk for this function. This is case insensitive.
 If you want to only load a single sample without the use of an input file, you have to set the following variables.
@@ -17,42 +17,49 @@
 patient
 samples_file = NULL
 
-"></head><body>
+"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>LoadingMAEGATK_typewise</h1>
-
+      <img src="" class="logo" alt=""><h1>LoadingMAEGATK_typewise</h1>
+      
       <div class="d-none name"><code>LoadingMAEGATK_typewise.Rd</code></div>
     </div>
 
@@ -86,74 +93,72 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-samples-file">samples_file<a class="anchor" aria-label="anchor" href="#arg-samples-file"></a></dt>
+    <dl><dt>samples_file</dt>
 <dd><p>Path to the csv file with the samples to be loaded.</p></dd>
 
 
-<dt id="arg-patient">patient<a class="anchor" aria-label="anchor" href="#arg-patient"></a></dt>
+<dt>patient</dt>
 <dd><p>The patient you want to load.</p></dd>
 
 
-<dt id="arg-samples-path">samples_path<a class="anchor" aria-label="anchor" href="#arg-samples-path"></a></dt>
+<dt>samples_path</dt>
 <dd><p>Path to the input folder.</p></dd>
 
 
-<dt id="arg-patient-column">patient_column<a class="anchor" aria-label="anchor" href="#arg-patient-column"></a></dt>
+<dt>patient_column</dt>
 <dd><p>The column that contains the patient information. Use merge, if all samples should be merged.</p></dd>
 
 
-<dt id="arg-type-use">type_use<a class="anchor" aria-label="anchor" href="#arg-type-use"></a></dt>
+<dt>type_use</dt>
 <dd><p>The type of input. Only rows that have the specified type will be loaded.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>The prefix you want use. Default: "chrM"</p></dd>
 
 
-<dt id="arg-min-cells">min_cells<a class="anchor" aria-label="anchor" href="#arg-min-cells"></a></dt>
+<dt>min_cells</dt>
 <dd><p>The minimum number of cells with coverage for a variant. Variants with coverage in less than this amount of cells are removed. Default = 2</p></dd>
 
 
-<dt id="arg-cells-include">cells_include<a class="anchor" aria-label="anchor" href="#arg-cells-include"></a></dt>
+<dt>cells_include</dt>
 <dd><p>A vector of cell barcodes. Only these cells will be retained.</p></dd>
 
 
-<dt id="arg-cells-exclude">cells_exclude<a class="anchor" aria-label="anchor" href="#arg-cells-exclude"></a></dt>
+<dt>cells_exclude</dt>
 <dd><p>A vector of cell barcodes. These cells will be removed from the output.</p></dd>
 
 
-<dt id="arg-barcodes-path">barcodes_path<a class="anchor" aria-label="anchor" href="#arg-barcodes-path"></a></dt>
+<dt>barcodes_path</dt>
 <dd><p>Path to the barcodes file tsv. Default = NULL</p></dd>
 
 
-<dt id="arg-cellbarcode-length">cellbarcode_length<a class="anchor" aria-label="anchor" href="#arg-cellbarcode-length"></a></dt>
+<dt>cellbarcode_length</dt>
 <dd><p>The length of the cell barcode. This should be the length of the actual barcode plus two for the suffix (-1). Default = 18</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
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+  
 
   </body></html>
 
diff --git a/docs/reference/LoadingRawMatrix_typewise.html b/docs/reference/LoadingRawMatrix_typewise.html
index d89736f..a2fa4a6 100644
--- a/docs/reference/LoadingRawMatrix_typewise.html
+++ b/docs/reference/LoadingRawMatrix_typewise.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>LoadingRawMatrix_typewise — LoadingRawMatrix_typewise • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="LoadingRawMatrix_typewise — LoadingRawMatrix_typewise"><meta name="description" content="A function to load a dense matrix of genotyping information and reformat it. Each matrix should have a column with the cell barcodes, one with the reference reads and one with the alternative reads.
-The type in the design matrix is used as the variant name."><meta property="og:description" content="A function to load a dense matrix of genotyping information and reformat it. Each matrix should have a column with the cell barcodes, one with the reference reads and one with the alternative reads.
-The type in the design matrix is used as the variant name."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A function to load a dense matrix of genotyping information and reformat it. Each matrix should have a column with the cell barcodes, one with the reference reads and one with the alternative reads.
+The type in the design matrix is used as the variant name."><title>LoadingRawMatrix_typewise — LoadingRawMatrix_typewise • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="LoadingRawMatrix_typewise — LoadingRawMatrix_typewise"><meta property="og:description" content="A function to load a dense matrix of genotyping information and reformat it. Each matrix should have a column with the cell barcodes, one with the reference reads and one with the alternative reads.
+The type in the design matrix is used as the variant name."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
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+    
 
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>LoadingRawMatrix_typewise</h1>
-
+      <img src="" class="logo" alt=""><h1>LoadingRawMatrix_typewise</h1>
+      
       <div class="d-none name"><code>LoadingRawMatrix_typewise.Rd</code></div>
     </div>
 
@@ -66,62 +73,60 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-samples-file">samples_file<a class="anchor" aria-label="anchor" href="#arg-samples-file"></a></dt>
+    <dl><dt>samples_file</dt>
 <dd><p>Path to the csv file with the samples to be loaded.</p></dd>
 
 
-<dt id="arg-patient">patient<a class="anchor" aria-label="anchor" href="#arg-patient"></a></dt>
+<dt>patient</dt>
 <dd><p>The patient you want to load.</p></dd>
 
 
-<dt id="arg-patient-column">patient_column<a class="anchor" aria-label="anchor" href="#arg-patient-column"></a></dt>
+<dt>patient_column</dt>
 <dd><p>The column that contains the patient information.</p></dd>
 
 
-<dt id="arg-variant-use">variant_use<a class="anchor" aria-label="anchor" href="#arg-variant-use"></a></dt>
+<dt>variant_use</dt>
 <dd><p>The variant of the respective matrices.</p></dd>
 
 
-<dt id="arg-cells-include">cells_include<a class="anchor" aria-label="anchor" href="#arg-cells-include"></a></dt>
+<dt>cells_include</dt>
 <dd><p>A vector of cell barcodes. Only these cells will be retained.</p></dd>
 
 
-<dt id="arg-cells-exclude">cells_exclude<a class="anchor" aria-label="anchor" href="#arg-cells-exclude"></a></dt>
+<dt>cells_exclude</dt>
 <dd><p>A vector of cell barcodes. These cells will be removed from the output.</p></dd>
 
 
-<dt id="arg-cellbarcode-length">cellbarcode_length<a class="anchor" aria-label="anchor" href="#arg-cellbarcode-length"></a></dt>
+<dt>cellbarcode_length</dt>
 <dd><p>The length of the cell barcode. This should be the length of the actual barcode plus two for the suffix (-1). Default = 18</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 
-<dt id="arg-samples-path">samples_path<a class="anchor" aria-label="anchor" href="#arg-samples-path"></a></dt>
+<dt>samples_path</dt>
 <dd><p>Path to the input folder. Must include a barcodes file.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
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+  
 
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diff --git a/docs/reference/LoadingVCF_typewise.html b/docs/reference/LoadingVCF_typewise.html
index cc8028c..d6b7674 100644
--- a/docs/reference/LoadingVCF_typewise.html
+++ b/docs/reference/LoadingVCF_typewise.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>LoadingVCF_typewise — LoadingVCF_typewise • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="LoadingVCF_typewise — LoadingVCF_typewise"><meta name="description" content="We load a cellwise pileup result from a VCF file.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We load a cellwise pileup result from a VCF file.
 If you want to only load a single sample without the use of an input file, you have to set the following variables.
 samples_path
 patient
@@ -7,7 +7,7 @@
 Note that the source column in the input file needs to be vcf for this function. This is case insensitive.
 It has happened that reads with an N allele were aligned. This can cause problems since these variants are typically not in variants lists.
 We can remove all of these variants by setting remove_N_alternative to TRUE (the default).
-Set this option to FALSE, if you really want to retain these variants."><meta property="og:description" content="We load a cellwise pileup result from a VCF file.
+Set this option to FALSE, if you really want to retain these variants."><title>LoadingVCF_typewise — LoadingVCF_typewise • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="LoadingVCF_typewise — LoadingVCF_typewise"><meta property="og:description" content="We load a cellwise pileup result from a VCF file.
 If you want to only load a single sample without the use of an input file, you have to set the following variables.
 samples_path
 patient
@@ -15,42 +15,49 @@
 Note that the source column in the input file needs to be vcf for this function. This is case insensitive.
 It has happened that reads with an N allele were aligned. This can cause problems since these variants are typically not in variants lists.
 We can remove all of these variants by setting remove_N_alternative to TRUE (the default).
-Set this option to FALSE, if you really want to retain these variants."></head><body>
+Set this option to FALSE, if you really want to retain these variants."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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+    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>LoadingVCF_typewise</h1>
-
+      <img src="" class="logo" alt=""><h1>LoadingVCF_typewise</h1>
+      
       <div class="d-none name"><code>LoadingVCF_typewise.Rd</code></div>
     </div>
 
@@ -86,78 +93,76 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-samples-file">samples_file<a class="anchor" aria-label="anchor" href="#arg-samples-file"></a></dt>
+    <dl><dt>samples_file</dt>
 <dd><p>Path to the csv file with the samples to be loaded.</p></dd>
 
 
-<dt id="arg-samples-path">samples_path<a class="anchor" aria-label="anchor" href="#arg-samples-path"></a></dt>
+<dt>samples_path</dt>
 <dd><p>Path to the input folder.</p></dd>
 
 
-<dt id="arg-vcf-path">vcf_path<a class="anchor" aria-label="anchor" href="#arg-vcf-path"></a></dt>
+<dt>vcf_path</dt>
 <dd><p>Path to the VCF file with the variants.</p></dd>
 
 
-<dt id="arg-patient">patient<a class="anchor" aria-label="anchor" href="#arg-patient"></a></dt>
+<dt>patient</dt>
 <dd><p>The patient you want to load.</p></dd>
 
 
-<dt id="arg-patient-column">patient_column<a class="anchor" aria-label="anchor" href="#arg-patient-column"></a></dt>
+<dt>patient_column</dt>
 <dd><p>The column that contains the patient information. Use merge, if all samples should be merged.</p></dd>
 
 
-<dt id="arg-type-use">type_use<a class="anchor" aria-label="anchor" href="#arg-type-use"></a></dt>
+<dt>type_use</dt>
 <dd><p>The type of input. Only rows that have the specified type will be loaded.</p></dd>
 
 
-<dt id="arg-min-reads">min_reads<a class="anchor" aria-label="anchor" href="#arg-min-reads"></a></dt>
+<dt>min_reads</dt>
 <dd><p>The minimum number of reads we want. Otherwise we treat this as a NoCall. Default = NULL.</p></dd>
 
 
-<dt id="arg-min-cells">min_cells<a class="anchor" aria-label="anchor" href="#arg-min-cells"></a></dt>
+<dt>min_cells</dt>
 <dd><p>The minimum number of cells for a variant. Otherwise, we will remove a variant. Default = 2.</p></dd>
 
 
-<dt id="arg-cells-include">cells_include<a class="anchor" aria-label="anchor" href="#arg-cells-include"></a></dt>
+<dt>cells_include</dt>
 <dd><p>A vector of cell barcodes. Only these cells will be retained.</p></dd>
 
 
-<dt id="arg-cells-exclude">cells_exclude<a class="anchor" aria-label="anchor" href="#arg-cells-exclude"></a></dt>
+<dt>cells_exclude</dt>
 <dd><p>A vector of cell barcodes. These cells will be removed from the output.</p></dd>
 
 
-<dt id="arg-remove-n-alternative">remove_N_alternative<a class="anchor" aria-label="anchor" href="#arg-remove-n-alternative"></a></dt>
+<dt>remove_N_alternative</dt>
 <dd><p>Remove all variants that have N as an alternative, see Description. Default = TRUE</p></dd>
 
 
-<dt id="arg-cellbarcode-length">cellbarcode_length<a class="anchor" aria-label="anchor" href="#arg-cellbarcode-length"></a></dt>
+<dt>cellbarcode_length</dt>
 <dd><p>The length of the cell barcode. This should be the length of the actual barcode plus two for the suffix (-1). Default = 18</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
-
+  
 
   </body></html>
 
diff --git a/docs/reference/LoadingVarTrix_typewise.html b/docs/reference/LoadingVarTrix_typewise.html
index 4f012de..b0e311d 100644
--- a/docs/reference/LoadingVarTrix_typewise.html
+++ b/docs/reference/LoadingVarTrix_typewise.html
@@ -1,52 +1,59 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>LoadingVarTrix_typewise — LoadingVarTrix_typewise • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="LoadingVarTrix_typewise — LoadingVarTrix_typewise"><meta name="description" content="When we load all the different types of results (scRNAseq/amplicon and MT/amplicon),
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="When we load all the different types of results (scRNAseq/amplicon and MT/amplicon),
 we might need extreme amounts of memory. To solve this issue, I will load each type separately.
 In a following function (AmpliconSupplementing), we can add the amplicon information to the
 scRNAseq information.
 The input file is a specifically formatted csv file with all the necessary information to run the analysis.
 Note that the source column in the input file needs to be vartrix for this function.
-This is hard coded and case insensitive."><meta property="og:description" content="When we load all the different types of results (scRNAseq/amplicon and MT/amplicon),
+This is hard coded and case insensitive."><title>LoadingVarTrix_typewise — LoadingVarTrix_typewise • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="LoadingVarTrix_typewise — LoadingVarTrix_typewise"><meta property="og:description" content="When we load all the different types of results (scRNAseq/amplicon and MT/amplicon),
 we might need extreme amounts of memory. To solve this issue, I will load each type separately.
 In a following function (AmpliconSupplementing), we can add the amplicon information to the
 scRNAseq information.
 The input file is a specifically formatted csv file with all the necessary information to run the analysis.
 Note that the source column in the input file needs to be vartrix for this function.
-This is hard coded and case insensitive."></head><body>
+This is hard coded and case insensitive."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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+    
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>LoadingVarTrix_typewise</h1>
-
+      <img src="" class="logo" alt=""><h1>LoadingVarTrix_typewise</h1>
+      
       <div class="d-none name"><code>LoadingVarTrix_typewise.Rd</code></div>
     </div>
 
@@ -82,82 +89,80 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-samples-file">samples_file<a class="anchor" aria-label="anchor" href="#arg-samples-file"></a></dt>
+    <dl><dt>samples_file</dt>
 <dd><p>Path to the csv file with the samples to be loaded.</p></dd>
 
 
-<dt id="arg-samples-path">samples_path<a class="anchor" aria-label="anchor" href="#arg-samples-path"></a></dt>
+<dt>samples_path</dt>
 <dd><p>Path to the input folder. Must include a barcodes file.</p></dd>
 
 
-<dt id="arg-barcodes-path">barcodes_path<a class="anchor" aria-label="anchor" href="#arg-barcodes-path"></a></dt>
+<dt>barcodes_path</dt>
 <dd><p>The path to the cell barcodes tsv. Default = NULL</p></dd>
 
 
-<dt id="arg-snp-path">snp_path<a class="anchor" aria-label="anchor" href="#arg-snp-path"></a></dt>
+<dt>snp_path</dt>
 <dd><p>Path to the SNP file used for VarTrix (SNV.loci.txt).</p></dd>
 
 
-<dt id="arg-vcf-path">vcf_path<a class="anchor" aria-label="anchor" href="#arg-vcf-path"></a></dt>
+<dt>vcf_path</dt>
 <dd><p>Path to the VCF file with the variants.</p></dd>
 
 
-<dt id="arg-patient">patient<a class="anchor" aria-label="anchor" href="#arg-patient"></a></dt>
+<dt>patient</dt>
 <dd><p>The patient you want to load.</p></dd>
 
 
-<dt id="arg-patient-column">patient_column<a class="anchor" aria-label="anchor" href="#arg-patient-column"></a></dt>
+<dt>patient_column</dt>
 <dd><p>The column that contains the patient information. Use merge, if all samples should be merged.</p></dd>
 
 
-<dt id="arg-type-use">type_use<a class="anchor" aria-label="anchor" href="#arg-type-use"></a></dt>
+<dt>type_use</dt>
 <dd><p>The type of input. Only rows that have the specified type will be loaded.</p></dd>
 
 
-<dt id="arg-min-reads">min_reads<a class="anchor" aria-label="anchor" href="#arg-min-reads"></a></dt>
+<dt>min_reads</dt>
 <dd><p>The minimum number of reads we want. Otherwise we treat this as a NoCall. Default = NULL.</p></dd>
 
 
-<dt id="arg-min-cells">min_cells<a class="anchor" aria-label="anchor" href="#arg-min-cells"></a></dt>
+<dt>min_cells</dt>
 <dd><p>The minimum number of cells for a variant. Otherwise, we will remove a variant. Default = 2.</p></dd>
 
 
-<dt id="arg-cells-include">cells_include<a class="anchor" aria-label="anchor" href="#arg-cells-include"></a></dt>
+<dt>cells_include</dt>
 <dd><p>A vector of cell barcodes. Only these cells will be retained.</p></dd>
 
 
-<dt id="arg-cells-exclude">cells_exclude<a class="anchor" aria-label="anchor" href="#arg-cells-exclude"></a></dt>
+<dt>cells_exclude</dt>
 <dd><p>A vector of cell barcodes. These cells will be removed from the output.</p></dd>
 
 
-<dt id="arg-cellbarcode-length">cellbarcode_length<a class="anchor" aria-label="anchor" href="#arg-cellbarcode-length"></a></dt>
+<dt>cellbarcode_length</dt>
 <dd><p>The length of the cell barcode. This should be the length of the actual barcode plus two for the suffix (-1). Default = 18</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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diff --git a/docs/reference/Merging_SE_list.html b/docs/reference/Merging_SE_list.html
index 58ac6bd..e84a19d 100644
--- a/docs/reference/Merging_SE_list.html
+++ b/docs/reference/Merging_SE_list.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Merging list of SummarizedExperiment objects. — Merging_SE_list • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Merging list of SummarizedExperiment objects. — Merging_SE_list"><meta name="description" content='This function is a wrapper for do.all("cbind", se).'><meta property="og:description" content='This function is a wrapper for do.all("cbind", se).'></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='This function is a wrapper for do.all("cbind", se).'><title>Merging list of SummarizedExperiment objects. — Merging_SE_list • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Merging list of SummarizedExperiment objects. — Merging_SE_list"><meta property="og:description" content='This function is a wrapper for do.all("cbind", se).'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+    
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>Merging list of SummarizedExperiment objects.</h1>
-
+      <img src="" class="logo" alt=""><h1>Merging list of SummarizedExperiment objects.</h1>
+      
       <div class="d-none name"><code>Merging_SE_list.Rd</code></div>
     </div>
 
@@ -49,30 +56,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">se<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>se</dt>
 <dd><p>SummarizedExperiment object</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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+  
 
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+  
 
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diff --git a/docs/reference/RowWiseSplit.html b/docs/reference/RowWiseSplit.html
index 37867d0..4244e23 100644
--- a/docs/reference/RowWiseSplit.html
+++ b/docs/reference/RowWiseSplit.html
@@ -1,44 +1,51 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>RowWiseSplit — RowWiseSplit • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RowWiseSplit — RowWiseSplit"><meta name="description" content="Performing the correlation or Fisher test association for a SummarizedExperiment object requires extreme amounts of memory.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Performing the correlation or Fisher test association for a SummarizedExperiment object requires extreme amounts of memory.
 To reduce the amount of memory necessary, we instead get the individual rows from the consensus assay.
-We can then remove the NoCalls (no reads) from the individual vectors, further reducing the amount of memory needed."><meta property="og:description" content="Performing the correlation or Fisher test association for a SummarizedExperiment object requires extreme amounts of memory.
+We can then remove the NoCalls (no reads) from the individual vectors, further reducing the amount of memory needed."><title>RowWiseSplit — RowWiseSplit • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RowWiseSplit — RowWiseSplit"><meta property="og:description" content="Performing the correlation or Fisher test association for a SummarizedExperiment object requires extreme amounts of memory.
 To reduce the amount of memory necessary, we instead get the individual rows from the consensus assay.
-We can then remove the NoCalls (no reads) from the individual vectors, further reducing the amount of memory needed."></head><body>
+We can then remove the NoCalls (no reads) from the individual vectors, further reducing the amount of memory needed."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>RowWiseSplit</h1>
-
+      <img src="" class="logo" alt=""><h1>RowWiseSplit</h1>
+      
       <div class="d-none name"><code>RowWiseSplit.Rd</code></div>
     </div>
 
@@ -55,38 +62,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">se<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>se</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-n-cores">n_cores<a class="anchor" aria-label="anchor" href="#arg-n-cores"></a></dt>
+<dt>n_cores</dt>
 <dd><p>Number of cores to use.</p></dd>
 
 
-<dt id="arg-remove-nocalls">remove_nocalls<a class="anchor" aria-label="anchor" href="#arg-remove-nocalls"></a></dt>
+<dt>remove_nocalls</dt>
 <dd><p>Do you want to remove NoCall cells?</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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+  
 
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+  
 
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diff --git a/docs/reference/SeparatingMatrixToList.html b/docs/reference/SeparatingMatrixToList.html
index d843515..e8bdd80 100644
--- a/docs/reference/SeparatingMatrixToList.html
+++ b/docs/reference/SeparatingMatrixToList.html
@@ -1,46 +1,53 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>SeparatingMatrixToList — SeparatingMatrixToList • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="SeparatingMatrixToList — SeparatingMatrixToList"><meta name="description" content="We separate a matrix of variant information to a list.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We separate a matrix of variant information to a list.
 Each variant is an entry in the list.
 NoCalls (cells with no reads covering a variant) can be removed.
-This function gets called by RowWiseSplit in return."><meta property="og:description" content="We separate a matrix of variant information to a list.
+This function gets called by RowWiseSplit in return."><title>SeparatingMatrixToList — SeparatingMatrixToList • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="SeparatingMatrixToList — SeparatingMatrixToList"><meta property="og:description" content="We separate a matrix of variant information to a list.
 Each variant is an entry in the list.
 NoCalls (cells with no reads covering a variant) can be removed.
-This function gets called by RowWiseSplit in return."></head><body>
+This function gets called by RowWiseSplit in return."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
-
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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+    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>SeparatingMatrixToList</h1>
-
+      <img src="" class="logo" alt=""><h1>SeparatingMatrixToList</h1>
+      
       <div class="d-none name"><code>SeparatingMatrixToList.Rd</code></div>
     </div>
 
@@ -58,38 +65,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-row-use">row_use<a class="anchor" aria-label="anchor" href="#arg-row-use"></a></dt>
+    <dl><dt>row_use</dt>
 <dd><p>The row the separate.</p></dd>
 
 
-<dt id="arg-total-matrix">total_matrix<a class="anchor" aria-label="anchor" href="#arg-total-matrix"></a></dt>
+<dt>total_matrix</dt>
 <dd><p>The matrix to be split.</p></dd>
 
 
-<dt id="arg-remove-nocalls">remove_nocalls<a class="anchor" aria-label="anchor" href="#arg-remove-nocalls"></a></dt>
+<dt>remove_nocalls</dt>
 <dd><p>Do you want to remove NoCall cells?</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
-
+  
 
   </body></html>
 
diff --git a/docs/reference/SetVariantInfo.html b/docs/reference/SetVariantInfo.html
index 988e33c..0a5d9f6 100644
--- a/docs/reference/SetVariantInfo.html
+++ b/docs/reference/SetVariantInfo.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>SetVariantInfo — SetVariantInfo • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="SetVariantInfo — SetVariantInfo"><meta name="description" content="We add the genotyping information for a set of variants to a Seurat object.
-The function returns a Seurat object with the values from the specified assay added as meta data."><meta property="og:description" content="We add the genotyping information for a set of variants to a Seurat object.
-The function returns a Seurat object with the values from the specified assay added as meta data."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We add the genotyping information for a set of variants to a Seurat object.
+The function returns a Seurat object with the values from the specified assay added as meta data."><title>SetVariantInfo — SetVariantInfo • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="SetVariantInfo — SetVariantInfo"><meta property="og:description" content="We add the genotyping information for a set of variants to a Seurat object.
+The function returns a Seurat object with the values from the specified assay added as meta data."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
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+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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-  </ul></li>
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-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>SetVariantInfo</h1>
-
+      <img src="" class="logo" alt=""><h1>SetVariantInfo</h1>
+      
       <div class="d-none name"><code>SetVariantInfo.Rd</code></div>
     </div>
 
@@ -59,50 +66,48 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-seurat-object">seurat_object<a class="anchor" aria-label="anchor" href="#arg-seurat-object"></a></dt>
+<dt>seurat_object</dt>
 <dd><p>The Seurat object.</p></dd>
 
 
-<dt id="arg-information">information<a class="anchor" aria-label="anchor" href="#arg-information"></a></dt>
+<dt>information</dt>
 <dd><p>The assay with the desired information. Default: consensus</p></dd>
 
 
-<dt id="arg-variants">variants<a class="anchor" aria-label="anchor" href="#arg-variants"></a></dt>
+<dt>variants</dt>
 <dd><p>A vector of variants.</p></dd>
 
 
-<dt id="arg-consensus-character">consensus_character<a class="anchor" aria-label="anchor" href="#arg-consensus-character"></a></dt>
+<dt>consensus_character</dt>
 <dd><p>Should the consensus information be save as a character value?</p></dd>
 
 
-<dt id="arg-consensus-group">consensus_group<a class="anchor" aria-label="anchor" href="#arg-consensus-group"></a></dt>
+<dt>consensus_group</dt>
 <dd><p>Should the consensus groups Alt and Both be merged? Has no effect if information is not consensus.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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diff --git a/docs/reference/UMIQC.html b/docs/reference/UMIQC.html
index b34bfde..5f05b9e 100644
--- a/docs/reference/UMIQC.html
+++ b/docs/reference/UMIQC.html
@@ -1,44 +1,51 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>UMIQC — UMIQC • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UMIQC — UMIQC"><meta name="description" content="We load the molecule_info.h5 file from CellRanger and plot the molecules by rank.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We load the molecule_info.h5 file from CellRanger and plot the molecules by rank.
 A molecule is defined as a combination of UMI and CB.
-The molecules are ranked by their number of replicates."><meta property="og:description" content="We load the molecule_info.h5 file from CellRanger and plot the molecules by rank.
+The molecules are ranked by their number of replicates."><title>UMIQC — UMIQC • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UMIQC — UMIQC"><meta property="og:description" content="We load the molecule_info.h5 file from CellRanger and plot the molecules by rank.
 A molecule is defined as a combination of UMI and CB.
-The molecules are ranked by their number of replicates."></head><body>
+The molecules are ranked by their number of replicates."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
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-
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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+    
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
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-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>UMIQC</h1>
-
+      <img src="" class="logo" alt=""><h1>UMIQC</h1>
+      
       <div class="d-none name"><code>UMIQC.Rd</code></div>
     </div>
 
@@ -67,70 +74,68 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-central-input-file">central_input_file<a class="anchor" aria-label="anchor" href="#arg-central-input-file"></a></dt>
+    <dl><dt>central_input_file</dt>
 <dd><p>Path to the csv file with the samples to be loaded.</p></dd>
 
 
-<dt id="arg-molecule-info-path">molecule_info_path<a class="anchor" aria-label="anchor" href="#arg-molecule-info-path"></a></dt>
+<dt>molecule_info_path</dt>
 <dd><p>Path to a single molecule_info file.</p></dd>
 
 
-<dt id="arg-subset-by-cbs">subset_by_cbs<a class="anchor" aria-label="anchor" href="#arg-subset-by-cbs"></a></dt>
+<dt>subset_by_cbs</dt>
 <dd><p>Should the list of cell barcodes from the molecule_info.h5 file be subset to a list of approved cell barcodes? Default: TRUE</p></dd>
 
 
-<dt id="arg-cellbarcodes-path">cellbarcodes_path<a class="anchor" aria-label="anchor" href="#arg-cellbarcodes-path"></a></dt>
+<dt>cellbarcodes_path</dt>
 <dd><p>Path to a cell barcodes file. Not used if the central input file is used.</p></dd>
 
 
-<dt id="arg-umi-length">umi_length<a class="anchor" aria-label="anchor" href="#arg-umi-length"></a></dt>
+<dt>umi_length</dt>
 <dd><p>The length of the UMI. Default = 12</p></dd>
 
 
-<dt id="arg-min-reads">min_reads<a class="anchor" aria-label="anchor" href="#arg-min-reads"></a></dt>
+<dt>min_reads</dt>
 <dd><p>The minimum number of reads per molecule.</p></dd>
 
 
-<dt id="arg-sep">sep<a class="anchor" aria-label="anchor" href="#arg-sep"></a></dt>
+<dt>sep</dt>
 <dd><p>The separator used in your samples_file. Default: ","</p></dd>
 
 
-<dt id="arg-samples-column">samples_column<a class="anchor" aria-label="anchor" href="#arg-samples-column"></a></dt>
+<dt>samples_column</dt>
 <dd><p>The column for the samples in your samples_file. Default: "sample"</p></dd>
 
 
-<dt id="arg-molecule-info-column">molecule_info_column<a class="anchor" aria-label="anchor" href="#arg-molecule-info-column"></a></dt>
+<dt>molecule_info_column</dt>
 <dd><p>The column for the paths to the molecule_info files in your samples_file. Default: "molecule_info"</p></dd>
 
 
-<dt id="arg-cellbarcode-column">cellbarcode_column<a class="anchor" aria-label="anchor" href="#arg-cellbarcode-column"></a></dt>
+<dt>cellbarcode_column</dt>
 <dd><p>The column for the paths to the cell barcodes files in your central input file. Default: "cells"</p></dd>
 
 
-<dt id="arg-add-x-suffix">add_10x_suffix<a class="anchor" aria-label="anchor" href="#arg-add-x-suffix"></a></dt>
+<dt>add_10x_suffix</dt>
 <dd><p>Should a suffix be added to the cell barcodes? Default to the 10X standard: "-1"</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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diff --git a/docs/reference/UMI_seq.html b/docs/reference/UMI_seq.html
index 6ae1fa3..b15a3b3 100644
--- a/docs/reference/UMI_seq.html
+++ b/docs/reference/UMI_seq.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>UMI_seq — UMI_seq • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UMI_seq — UMI_seq"><meta name="description" content="This function converts the numeric UMI representation found in a 10X molecule_info.h5 file to a character string."><meta property="og:description" content="This function converts the numeric UMI representation found in a 10X molecule_info.h5 file to a character string."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function converts the numeric UMI representation found in a 10X molecule_info.h5 file to a character string."><title>UMI_seq — UMI_seq • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UMI_seq — UMI_seq"><meta property="og:description" content="This function converts the numeric UMI representation found in a 10X molecule_info.h5 file to a character string."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+    
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>UMI_seq</h1>
-
+      <img src="" class="logo" alt=""><h1>UMI_seq</h1>
+      
       <div class="d-none name"><code>UMI_seq.Rd</code></div>
     </div>
 
@@ -49,34 +56,32 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-number">number<a class="anchor" aria-label="anchor" href="#arg-number"></a></dt>
+    <dl><dt>number</dt>
 <dd><p>The numeric expression of a UMI.</p></dd>
 
 
-<dt id="arg-umi-length">umi_length<a class="anchor" aria-label="anchor" href="#arg-umi-length"></a></dt>
+<dt>umi_length</dt>
 <dd><p>The length of the UMI. Default = 12</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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     </footer></div>
 
+  
 
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+  
 
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diff --git a/docs/reference/VariantBurden.html b/docs/reference/VariantBurden.html
index 0f59e30..0d2f85b 100644
--- a/docs/reference/VariantBurden.html
+++ b/docs/reference/VariantBurden.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantBurden — VariantBurden • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantBurden — VariantBurden"><meta name="description" content="Calculate the variant burden per cell.
-We simply sum up the MAF values per cell."><meta property="og:description" content="Calculate the variant burden per cell.
-We simply sum up the MAF values per cell."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculate the variant burden per cell.
+We simply sum up the MAF values per cell."><title>VariantBurden — VariantBurden • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantBurden — VariantBurden"><meta property="og:description" content="Calculate the variant burden per cell.
+We simply sum up the MAF values per cell."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>VariantBurden</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantBurden</h1>
+      
       <div class="d-none name"><code>VariantBurden.Rd</code></div>
     </div>
 
@@ -52,30 +59,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">se<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>se</dt>
 <dd><p>SummarizedExperiment object</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
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+  
 
   </body></html>
 
diff --git a/docs/reference/VariantCloneSizeThresholding.html b/docs/reference/VariantCloneSizeThresholding.html
index ba8d66b..bb210f5 100644
--- a/docs/reference/VariantCloneSizeThresholding.html
+++ b/docs/reference/VariantCloneSizeThresholding.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantCloneSizeThresholding — VariantCloneSizeThresholding • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantCloneSizeThresholding — VariantCloneSizeThresholding"><meta name="description" content="We get variants of interest using a clone size thresholding.
-Source: https://github.com/petervangalen/MAESTER-2021"><meta property="og:description" content="We get variants of interest using a clone size thresholding.
-Source: https://github.com/petervangalen/MAESTER-2021"></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We get variants of interest using a clone size thresholding.
+Source: https://github.com/petervangalen/MAESTER-2021"><title>VariantCloneSizeThresholding — VariantCloneSizeThresholding • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantCloneSizeThresholding — VariantCloneSizeThresholding"><meta property="og:description" content="We get variants of interest using a clone size thresholding.
+Source: https://github.com/petervangalen/MAESTER-2021"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+    
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
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+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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-
-      <h1>VariantCloneSizeThresholding</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantCloneSizeThresholding</h1>
+      
       <div class="d-none name"><code>VariantCloneSizeThresholding.Rd</code></div>
     </div>
 
@@ -59,50 +66,48 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-min-coverage">min_coverage<a class="anchor" aria-label="anchor" href="#arg-min-coverage"></a></dt>
+<dt>min_coverage</dt>
 <dd><p>Minimum coverage a variant needs to have.</p></dd>
 
 
-<dt id="arg-fraction-negative-cells">fraction_negative_cells<a class="anchor" aria-label="anchor" href="#arg-fraction-negative-cells"></a></dt>
+<dt>fraction_negative_cells</dt>
 <dd><p>The fraction of negative cells needed.</p></dd>
 
 
-<dt id="arg-min-clone-size">min_clone_size<a class="anchor" aria-label="anchor" href="#arg-min-clone-size"></a></dt>
+<dt>min_clone_size</dt>
 <dd><p>minimum number of cells.</p></dd>
 
 
-<dt id="arg-vaf-threshold">vaf_threshold<a class="anchor" aria-label="anchor" href="#arg-vaf-threshold"></a></dt>
+<dt>vaf_threshold</dt>
 <dd><p>Variant Allele Threshold. Cells above this threshold are considered mutated.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+  
 
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+  
 
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diff --git a/docs/reference/VariantCorrelationHeatmap.html b/docs/reference/VariantCorrelationHeatmap.html
index 7fe425d..850fc2e 100644
--- a/docs/reference/VariantCorrelationHeatmap.html
+++ b/docs/reference/VariantCorrelationHeatmap.html
@@ -1,44 +1,51 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantCorrelationHeatmap — VariantCorrelationHeatmap • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantCorrelationHeatmap — VariantCorrelationHeatmap"><meta name="description" content="We generate a heatmap showing the correlation of somatic variants with the MT variants.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We generate a heatmap showing the correlation of somatic variants with the MT variants.
 Packages I want to remove. I cannot see where they are used.
-ggplot2 parallel rcompanion tidyr"><meta property="og:description" content="We generate a heatmap showing the correlation of somatic variants with the MT variants.
+ggplot2 parallel rcompanion tidyr"><title>VariantCorrelationHeatmap — VariantCorrelationHeatmap • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantCorrelationHeatmap — VariantCorrelationHeatmap"><meta property="og:description" content="We generate a heatmap showing the correlation of somatic variants with the MT variants.
 Packages I want to remove. I cannot see where they are used.
-ggplot2 parallel rcompanion tidyr"></head><body>
+ggplot2 parallel rcompanion tidyr"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
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-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
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 </nav><div class="container template-reference-topic">
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   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>VariantCorrelationHeatmap</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantCorrelationHeatmap</h1>
+      
       <div class="d-none name"><code>VariantCorrelationHeatmap.Rd</code></div>
     </div>
 
@@ -65,62 +72,60 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-correlation-results">correlation_results<a class="anchor" aria-label="anchor" href="#arg-correlation-results"></a></dt>
+    <dl><dt>correlation_results</dt>
 <dd><p>Data.frame with the correlation results.</p></dd>
 
 
-<dt id="arg-output-path">output_path<a class="anchor" aria-label="anchor" href="#arg-output-path"></a></dt>
+<dt>output_path</dt>
 <dd><p>Path to the output folder.</p></dd>
 
 
-<dt id="arg-patient">patient<a class="anchor" aria-label="anchor" href="#arg-patient"></a></dt>
+<dt>patient</dt>
 <dd><p>The patient for this heatmap.</p></dd>
 
 
-<dt id="arg-min-alt-cells">min_alt_cells<a class="anchor" aria-label="anchor" href="#arg-min-alt-cells"></a></dt>
+<dt>min_alt_cells</dt>
 <dd><p>Minimum number of mutated cells needed, otherwise a correlation will not be plotted.</p></dd>
 
 
-<dt id="arg-min-correlation">min_correlation<a class="anchor" aria-label="anchor" href="#arg-min-correlation"></a></dt>
+<dt>min_correlation</dt>
 <dd><p>Minimum correlation needed.</p></dd>
 
 
-<dt id="arg-width-use">width_use<a class="anchor" aria-label="anchor" href="#arg-width-use"></a></dt>
+<dt>width_use</dt>
 <dd><p>Width of the heatmap in px.</p></dd>
 
 
-<dt id="arg-height-use">height_use<a class="anchor" aria-label="anchor" href="#arg-height-use"></a></dt>
+<dt>height_use</dt>
 <dd><p>Height of the heatmap in px.</p></dd>
 
 
-<dt id="arg-padding-use">padding_use<a class="anchor" aria-label="anchor" href="#arg-padding-use"></a></dt>
+<dt>padding_use</dt>
 <dd><p>Space around the heatmap in mm. If this is to low, the variant names might be cut off.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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diff --git a/docs/reference/VariantFisherTestHeatmap.html b/docs/reference/VariantFisherTestHeatmap.html
index e5d7615..4137675 100644
--- a/docs/reference/VariantFisherTestHeatmap.html
+++ b/docs/reference/VariantFisherTestHeatmap.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantFisherTestHeatmap — VariantFisherTestHeatmap • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantFisherTestHeatmap — VariantFisherTestHeatmap"><meta name="description" content="We generate a heatmap showing the Fisher test of somatic variants with the MT variants.
-Packages I want to remove."><meta property="og:description" content="We generate a heatmap showing the Fisher test of somatic variants with the MT variants.
-Packages I want to remove."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We generate a heatmap showing the Fisher test of somatic variants with the MT variants.
+Packages I want to remove."><title>VariantFisherTestHeatmap — VariantFisherTestHeatmap • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantFisherTestHeatmap — VariantFisherTestHeatmap"><meta property="og:description" content="We generate a heatmap showing the Fisher test of somatic variants with the MT variants.
+Packages I want to remove."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
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+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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-
-      <h1>VariantFisherTestHeatmap</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantFisherTestHeatmap</h1>
+      
       <div class="d-none name"><code>VariantFisherTestHeatmap.Rd</code></div>
     </div>
 
@@ -58,46 +65,44 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-fisher-results">fisher_results<a class="anchor" aria-label="anchor" href="#arg-fisher-results"></a></dt>
+    <dl><dt>fisher_results</dt>
 <dd><p>Data.frame with the correlation results.</p></dd>
 
 
-<dt id="arg-patient">patient<a class="anchor" aria-label="anchor" href="#arg-patient"></a></dt>
+<dt>patient</dt>
 <dd><p>The patient for this heatmap.</p></dd>
 
 
-<dt id="arg-min-alt-cells">min_alt_cells<a class="anchor" aria-label="anchor" href="#arg-min-alt-cells"></a></dt>
+<dt>min_alt_cells</dt>
 <dd><p>Minimum number of mutated cells needed, otherwise an association will not be plotted.</p></dd>
 
 
-<dt id="arg-min-oddsratio">min_oddsratio<a class="anchor" aria-label="anchor" href="#arg-min-oddsratio"></a></dt>
+<dt>min_oddsratio</dt>
 <dd><p>Minimum correlation needed.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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diff --git a/docs/reference/VariantQuantileThresholding_Combined.html b/docs/reference/VariantQuantileThresholding_Combined.html
index 361f925..d22a31b 100644
--- a/docs/reference/VariantQuantileThresholding_Combined.html
+++ b/docs/reference/VariantQuantileThresholding_Combined.html
@@ -1,46 +1,53 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined"><meta name="description" content="We get variants of interest using the quantile thresholding. This function combines the functions VariantSelection_Quantile, VariantSelection_Group and VariantSelection_TopCells.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We get variants of interest using the quantile thresholding. This function combines the functions VariantSelection_Quantile, VariantSelection_Group and VariantSelection_TopCells.
 If you use top_cells and top_VAF, you have to only supply one quantil value (quantiles = 0.9, thresholds = 0).
 This function is adapted from the Peter van Galen.
-Source: https://github.com/petervangalen/MAESTER-2021"><meta property="og:description" content="We get variants of interest using the quantile thresholding. This function combines the functions VariantSelection_Quantile, VariantSelection_Group and VariantSelection_TopCells.
+Source: https://github.com/petervangalen/MAESTER-2021"><title>VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined"><meta property="og:description" content="We get variants of interest using the quantile thresholding. This function combines the functions VariantSelection_Quantile, VariantSelection_Group and VariantSelection_TopCells.
 If you use top_cells and top_VAF, you have to only supply one quantil value (quantiles = 0.9, thresholds = 0).
 This function is adapted from the Peter van Galen.
-Source: https://github.com/petervangalen/MAESTER-2021"></head><body>
+Source: https://github.com/petervangalen/MAESTER-2021"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-      <h1>VariantQuantileThresholding_Combined</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantQuantileThresholding_Combined</h1>
+      
       <div class="d-none name"><code>VariantQuantileThresholding_Combined.Rd</code></div>
     </div>
 
@@ -73,82 +80,80 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-min-coverage">min_coverage<a class="anchor" aria-label="anchor" href="#arg-min-coverage"></a></dt>
+<dt>min_coverage</dt>
 <dd><p>Minimum coverage needed.</p></dd>
 
 
-<dt id="arg-quantiles">quantiles<a class="anchor" aria-label="anchor" href="#arg-quantiles"></a></dt>
+<dt>quantiles</dt>
 <dd><p>The lower and upper quantile you want to use.</p></dd>
 
 
-<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a></dt>
+<dt>thresholds</dt>
 <dd><p>The VAF thresholds you want to use for the quantiles.</p></dd>
 
 
-<dt id="arg-top-cells">top_cells<a class="anchor" aria-label="anchor" href="#arg-top-cells"></a></dt>
+<dt>top_cells</dt>
 <dd><p>The number of cells with at least top_VAF percent for a variant.</p></dd>
 
 
-<dt id="arg-top-vaf">top_VAF<a class="anchor" aria-label="anchor" href="#arg-top-vaf"></a></dt>
+<dt>top_VAF</dt>
 <dd><p>The VAF for the top cells.</p></dd>
 
 
-<dt id="arg-min-quality">min_quality<a class="anchor" aria-label="anchor" href="#arg-min-quality"></a></dt>
+<dt>min_quality</dt>
 <dd><p>The minimum quality you want for the Variants of Interest. Can be ignored by setting it to NULL.</p></dd>
 
 
-<dt id="arg-mean-allele-frequency">mean_allele_frequency<a class="anchor" aria-label="anchor" href="#arg-mean-allele-frequency"></a></dt>
+<dt>mean_allele_frequency</dt>
 <dd><p>The minimum mean allele frequency. Default = 0</p></dd>
 
 
-<dt id="arg-group-of-interest">group_of_interest<a class="anchor" aria-label="anchor" href="#arg-group-of-interest"></a></dt>
+<dt>group_of_interest</dt>
 <dd><p>The column data that divides the cells.</p></dd>
 
 
-<dt id="arg-group-">group1<a class="anchor" aria-label="anchor" href="#arg-group-"></a></dt>
+<dt>group1</dt>
 <dd><p>The first group of interest. If set, the quantiles are only calculated for this group.</p></dd>
 
 
-<dt id="arg-group-">group2<a class="anchor" aria-label="anchor" href="#arg-group-"></a></dt>
+<dt>group2</dt>
 <dd><p>The second group of interest.</p></dd>
 
 
-<dt id="arg-group-factor">group_factor<a class="anchor" aria-label="anchor" href="#arg-group-factor"></a></dt>
+<dt>group_factor</dt>
 <dd><p>How much higher has the mean allele frequency to be in group 1 when compared to group 2?</p></dd>
 
 
-<dt id="arg-remove-nocall">remove_nocall<a class="anchor" aria-label="anchor" href="#arg-remove-nocall"></a></dt>
+<dt>remove_nocall</dt>
 <dd><p>Should NoCall cells (consensus = 0) be disregarded during the analysis?</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
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+  
 
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diff --git a/docs/reference/VariantSelection_Group.html b/docs/reference/VariantSelection_Group.html
index 1fa875e..8e4c2ce 100644
--- a/docs/reference/VariantSelection_Group.html
+++ b/docs/reference/VariantSelection_Group.html
@@ -1,44 +1,51 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantSelection_Group — VariantSelection_Group • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantSelection_Group — VariantSelection_Group"><meta name="description" content="We get variants of interest by selecting variants with a high VAF difference between two groups.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We get variants of interest by selecting variants with a high VAF difference between two groups.
 This function is adapted from the Peter van Galen.
-Source: https://github.com/petervangalen/MAESTER-2021"><meta property="og:description" content="We get variants of interest by selecting variants with a high VAF difference between two groups.
+Source: https://github.com/petervangalen/MAESTER-2021"><title>VariantSelection_Group — VariantSelection_Group • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantSelection_Group — VariantSelection_Group"><meta property="og:description" content="We get variants of interest by selecting variants with a high VAF difference between two groups.
 This function is adapted from the Peter van Galen.
-Source: https://github.com/petervangalen/MAESTER-2021"></head><body>
+Source: https://github.com/petervangalen/MAESTER-2021"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+<![endif]--></head><body>
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+    
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
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+</li>
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+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>VariantSelection_Group</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantSelection_Group</h1>
+      
       <div class="d-none name"><code>VariantSelection_Group.Rd</code></div>
     </div>
 
@@ -68,74 +75,72 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-min-coverage">min_coverage<a class="anchor" aria-label="anchor" href="#arg-min-coverage"></a></dt>
+<dt>min_coverage</dt>
 <dd><p>Minimum coverage needed.</p></dd>
 
 
-<dt id="arg-quantiles">quantiles<a class="anchor" aria-label="anchor" href="#arg-quantiles"></a></dt>
+<dt>quantiles</dt>
 <dd><p>The lower and upper quantile you want to use.</p></dd>
 
 
-<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a></dt>
+<dt>thresholds</dt>
 <dd><p>The VAF thresholds you want to use for the quantiles.</p></dd>
 
 
-<dt id="arg-min-quality">min_quality<a class="anchor" aria-label="anchor" href="#arg-min-quality"></a></dt>
+<dt>min_quality</dt>
 <dd><p>The minimum quality you want for the Variants of Interest. Can be ignored by setting it to NULL.</p></dd>
 
 
-<dt id="arg-mean-allele-frequency">mean_allele_frequency<a class="anchor" aria-label="anchor" href="#arg-mean-allele-frequency"></a></dt>
+<dt>mean_allele_frequency</dt>
 <dd><p>The minimum mean allele frequency. Default = 0</p></dd>
 
 
-<dt id="arg-group-of-interest">group_of_interest<a class="anchor" aria-label="anchor" href="#arg-group-of-interest"></a></dt>
+<dt>group_of_interest</dt>
 <dd><p>The column data that divides the cells.</p></dd>
 
 
-<dt id="arg-group-">group1<a class="anchor" aria-label="anchor" href="#arg-group-"></a></dt>
+<dt>group1</dt>
 <dd><p>The first group of interest. If set, the quantiles are only calculated for this group.</p></dd>
 
 
-<dt id="arg-group-">group2<a class="anchor" aria-label="anchor" href="#arg-group-"></a></dt>
+<dt>group2</dt>
 <dd><p>The second group of interest.</p></dd>
 
 
-<dt id="arg-group-factor">group_factor<a class="anchor" aria-label="anchor" href="#arg-group-factor"></a></dt>
+<dt>group_factor</dt>
 <dd><p>How much higher has the mean allele frequency to be in group 1 when compared to group 2?</p></dd>
 
 
-<dt id="arg-remove-nocall">remove_nocall<a class="anchor" aria-label="anchor" href="#arg-remove-nocall"></a></dt>
+<dt>remove_nocall</dt>
 <dd><p>Should NoCall cells (consensus = 0) be disregarded during the analysis?</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/VariantSelection_Quantile.html b/docs/reference/VariantSelection_Quantile.html
index 0deeb4c..3f7fff3 100644
--- a/docs/reference/VariantSelection_Quantile.html
+++ b/docs/reference/VariantSelection_Quantile.html
@@ -1,44 +1,51 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantSelection_Quantile — VariantSelection_Quantile • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantSelection_Quantile — VariantSelection_Quantile"><meta name="description" content="We get variants of interest using the quantile thresholding.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We get variants of interest using the quantile thresholding.
 This function is adapted from the Peter van Galen.
-Source: https://github.com/petervangalen/MAESTER-2021"><meta property="og:description" content="We get variants of interest using the quantile thresholding.
+Source: https://github.com/petervangalen/MAESTER-2021"><title>VariantSelection_Quantile — VariantSelection_Quantile • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantSelection_Quantile — VariantSelection_Quantile"><meta property="og:description" content="We get variants of interest using the quantile thresholding.
 This function is adapted from the Peter van Galen.
-Source: https://github.com/petervangalen/MAESTER-2021"></head><body>
+Source: https://github.com/petervangalen/MAESTER-2021"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
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 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>VariantSelection_Quantile</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantSelection_Quantile</h1>
+      
       <div class="d-none name"><code>VariantSelection_Quantile.Rd</code></div>
     </div>
 
@@ -64,58 +71,56 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-min-coverage">min_coverage<a class="anchor" aria-label="anchor" href="#arg-min-coverage"></a></dt>
+<dt>min_coverage</dt>
 <dd><p>Minimum coverage needed.</p></dd>
 
 
-<dt id="arg-quantiles">quantiles<a class="anchor" aria-label="anchor" href="#arg-quantiles"></a></dt>
+<dt>quantiles</dt>
 <dd><p>The lower and upper quantile you want to use.</p></dd>
 
 
-<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a></dt>
+<dt>thresholds</dt>
 <dd><p>The VAF thresholds you want to use for the quantiles.</p></dd>
 
 
-<dt id="arg-min-quality">min_quality<a class="anchor" aria-label="anchor" href="#arg-min-quality"></a></dt>
+<dt>min_quality</dt>
 <dd><p>The minimum quality you want for the Variants of Interest. Can be ignored by setting it to NULL.</p></dd>
 
 
-<dt id="arg-mean-allele-frequency">mean_allele_frequency<a class="anchor" aria-label="anchor" href="#arg-mean-allele-frequency"></a></dt>
+<dt>mean_allele_frequency</dt>
 <dd><p>The minimum mean allele frequency. Default = 0</p></dd>
 
 
-<dt id="arg-remove-nocall">remove_nocall<a class="anchor" aria-label="anchor" href="#arg-remove-nocall"></a></dt>
+<dt>remove_nocall</dt>
 <dd><p>Should NoCall cells (consensus = 0) be disregarded during the analysis?</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+  
 
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+  
 
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diff --git a/docs/reference/VariantSelection_TopCells.html b/docs/reference/VariantSelection_TopCells.html
index 662fac5..8204361 100644
--- a/docs/reference/VariantSelection_TopCells.html
+++ b/docs/reference/VariantSelection_TopCells.html
@@ -1,44 +1,51 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantSelection_TopCells — VariantSelection_TopCells • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantSelection_TopCells — VariantSelection_TopCells"><meta name="description" content="We get variants of interest by selecting a small number of cells with a high VAF for a variant.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We get variants of interest by selecting a small number of cells with a high VAF for a variant.
 This function is adapted from the Peter van Galen.
-Source: https://github.com/petervangalen/MAESTER-2021"><meta property="og:description" content="We get variants of interest by selecting a small number of cells with a high VAF for a variant.
+Source: https://github.com/petervangalen/MAESTER-2021"><title>VariantSelection_TopCells — VariantSelection_TopCells • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantSelection_TopCells — VariantSelection_TopCells"><meta property="og:description" content="We get variants of interest by selecting a small number of cells with a high VAF for a variant.
 This function is adapted from the Peter van Galen.
-Source: https://github.com/petervangalen/MAESTER-2021"></head><body>
+Source: https://github.com/petervangalen/MAESTER-2021"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
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-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>VariantSelection_TopCells</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantSelection_TopCells</h1>
+      
       <div class="d-none name"><code>VariantSelection_TopCells.Rd</code></div>
     </div>
 
@@ -65,54 +72,52 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-min-coverage">min_coverage<a class="anchor" aria-label="anchor" href="#arg-min-coverage"></a></dt>
+<dt>min_coverage</dt>
 <dd><p>Minimum coverage needed.</p></dd>
 
 
-<dt id="arg-quantiles">quantiles<a class="anchor" aria-label="anchor" href="#arg-quantiles"></a></dt>
+<dt>quantiles</dt>
 <dd><p>The lower and upper quantile you want to use.</p></dd>
 
 
-<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a></dt>
+<dt>thresholds</dt>
 <dd><p>The VAF thresholds you want to use for the quantiles.</p></dd>
 
 
-<dt id="arg-min-quality">min_quality<a class="anchor" aria-label="anchor" href="#arg-min-quality"></a></dt>
+<dt>min_quality</dt>
 <dd><p>The minimum quality you want for the Variants of Interest. Can be ignored by setting it to NULL.</p></dd>
 
 
-<dt id="arg-remove-nocall">remove_nocall<a class="anchor" aria-label="anchor" href="#arg-remove-nocall"></a></dt>
+<dt>remove_nocall</dt>
 <dd><p>Should NoCall cells (consensus = 0) be disregarded during the analysis?</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
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+  
 
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diff --git a/docs/reference/VariantWiseCorrelation.html b/docs/reference/VariantWiseCorrelation.html
index a3014a8..97a386a 100644
--- a/docs/reference/VariantWiseCorrelation.html
+++ b/docs/reference/VariantWiseCorrelation.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantWiseCorrelation — VariantWiseCorrelation • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantWiseCorrelation — VariantWiseCorrelation"><meta name="description" content="We correlate the variants with each other using the Pearson correlation.
-This function calls CalculateCorrelationPValue to perform the actual correlation."><meta property="og:description" content="We correlate the variants with each other using the Pearson correlation.
-This function calls CalculateCorrelationPValue to perform the actual correlation."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We correlate the variants with each other using the Pearson correlation.
+This function calls CalculateCorrelationPValue to perform the actual correlation."><title>VariantWiseCorrelation — VariantWiseCorrelation • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantWiseCorrelation — VariantWiseCorrelation"><meta property="og:description" content="We correlate the variants with each other using the Pearson correlation.
+This function calls CalculateCorrelationPValue to perform the actual correlation."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>VariantWiseCorrelation</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantWiseCorrelation</h1>
+      
       <div class="d-none name"><code>VariantWiseCorrelation.Rd</code></div>
     </div>
 
@@ -57,42 +64,40 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-variants-list">variants_list<a class="anchor" aria-label="anchor" href="#arg-variants-list"></a></dt>
+    <dl><dt>variants_list</dt>
 <dd><p>List of fraction values.</p></dd>
 
 
-<dt id="arg-n-cores">n_cores<a class="anchor" aria-label="anchor" href="#arg-n-cores"></a></dt>
+<dt>n_cores</dt>
 <dd><p>Number of cores you want to use. Numeric.</p></dd>
 
 
-<dt id="arg-p-value-adjustment">p_value_adjustment<a class="anchor" aria-label="anchor" href="#arg-p-value-adjustment"></a></dt>
+<dt>p_value_adjustment</dt>
 <dd><p>Method for P value adjustment. See p.adjust for details.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/VariantWiseFisherTest.html b/docs/reference/VariantWiseFisherTest.html
index 86b133b..30ee215 100644
--- a/docs/reference/VariantWiseFisherTest.html
+++ b/docs/reference/VariantWiseFisherTest.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VariantWiseFisherTest — VariantWiseFisherTest • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantWiseFisherTest — VariantWiseFisherTest"><meta name="description" content="We perform the Fisher test to determine which variants are associated.
-This function calls CalculateFisherTestPValue to perform the actual testing."><meta property="og:description" content="We perform the Fisher test to determine which variants are associated.
-This function calls CalculateFisherTestPValue to perform the actual testing."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We perform the Fisher test to determine which variants are associated.
+This function calls CalculateFisherTestPValue to perform the actual testing."><title>VariantWiseFisherTest — VariantWiseFisherTest • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VariantWiseFisherTest — VariantWiseFisherTest"><meta property="og:description" content="We perform the Fisher test to determine which variants are associated.
+This function calls CalculateFisherTestPValue to perform the actual testing."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>VariantWiseFisherTest</h1>
-
+      <img src="" class="logo" alt=""><h1>VariantWiseFisherTest</h1>
+      
       <div class="d-none name"><code>VariantWiseFisherTest.Rd</code></div>
     </div>
 
@@ -57,42 +64,40 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-variants-list">variants_list<a class="anchor" aria-label="anchor" href="#arg-variants-list"></a></dt>
+    <dl><dt>variants_list</dt>
 <dd><p>List of fraction values.</p></dd>
 
 
-<dt id="arg-n-cores">n_cores<a class="anchor" aria-label="anchor" href="#arg-n-cores"></a></dt>
+<dt>n_cores</dt>
 <dd><p>Number of cores you want to use. Numeric.</p></dd>
 
 
-<dt id="arg-p-value-adjustment">p_value_adjustment<a class="anchor" aria-label="anchor" href="#arg-p-value-adjustment"></a></dt>
+<dt>p_value_adjustment</dt>
 <dd><p>Method for P value adjustment. See p.adjust for details.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt>verbose</dt>
 <dd><p>Should the function be verbose? Default = TRUE</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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+  
 
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diff --git a/docs/reference/char_to_numeric.html b/docs/reference/char_to_numeric.html
index bd524ca..2cd5006 100644
--- a/docs/reference/char_to_numeric.html
+++ b/docs/reference/char_to_numeric.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>char_to_numeric — char_to_numeric • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="char_to_numeric — char_to_numeric"><meta name="description" content="A function to convert the heterozygous/homozygous information from the VCF to the consensus information from VarTrix.
-It is only used in LoadingVCF_typewise.R."><meta property="og:description" content="A function to convert the heterozygous/homozygous information from the VCF to the consensus information from VarTrix.
-It is only used in LoadingVCF_typewise.R."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A function to convert the heterozygous/homozygous information from the VCF to the consensus information from VarTrix.
+It is only used in LoadingVCF_typewise.R."><title>char_to_numeric — char_to_numeric • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="char_to_numeric — char_to_numeric"><meta property="og:description" content="A function to convert the heterozygous/homozygous information from the VCF to the consensus information from VarTrix.
+It is only used in LoadingVCF_typewise.R."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
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+      <img src="" class="logo" alt=""><h1>char_to_numeric</h1>
+      
       <div class="d-none name"><code>char_to_numeric.Rd</code></div>
     </div>
 
@@ -52,30 +59,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-char-value">char_value<a class="anchor" aria-label="anchor" href="#arg-char-value"></a></dt>
+    <dl><dt>char_value</dt>
 <dd><p>What is the genotype encoding you want to convert?</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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diff --git a/docs/reference/combine_NAMES.html b/docs/reference/combine_NAMES.html
index c6e616a..699da63 100644
--- a/docs/reference/combine_NAMES.html
+++ b/docs/reference/combine_NAMES.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>combine_NAMES — combine_NAMES • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="combine_NAMES — combine_NAMES"><meta name="description" content="We combine two vectors of names."><meta property="og:description" content="We combine two vectors of names."></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We combine two vectors of names."><title>combine_NAMES — combine_NAMES • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="combine_NAMES — combine_NAMES"><meta property="og:description" content="We combine two vectors of names."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
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   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>combine_NAMES</h1>
-
+      <img src="" class="logo" alt=""><h1>combine_NAMES</h1>
+      
       <div class="d-none name"><code>combine_NAMES.Rd</code></div>
     </div>
 
@@ -49,34 +56,32 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+    <dl><dt>x</dt>
 <dd><p>First vector of names.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt>y</dt>
 <dd><p>Second vector of names.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+  
 
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diff --git a/docs/reference/combine_SparseMatrix.html b/docs/reference/combine_SparseMatrix.html
index eeb3a24..57aac79 100644
--- a/docs/reference/combine_SparseMatrix.html
+++ b/docs/reference/combine_SparseMatrix.html
@@ -1,40 +1,47 @@
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-      <h1>combine_sparseMatrix</h1>
-
+      <img src="" class="logo" alt=""><h1>combine_sparseMatrix</h1>
+      
       <div class="d-none name"><code>combine_SparseMatrix.Rd</code></div>
     </div>
 
@@ -49,34 +56,32 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-matrix-">matrix_1<a class="anchor" aria-label="anchor" href="#arg-matrix-"></a></dt>
+    <dl><dt>matrix_1</dt>
 <dd><p>Your first sparse matrix.</p></dd>
 
 
-<dt id="arg-matrix-">matrix_2<a class="anchor" aria-label="anchor" href="#arg-matrix-"></a></dt>
+<dt>matrix_2</dt>
 <dd><p>Your second matrix.</p></dd>
 
 </dl></div>
 
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 </div>
 
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diff --git a/docs/reference/computeAFMutMatrix.html b/docs/reference/computeAFMutMatrix.html
index 0b85079..72b43a5 100644
--- a/docs/reference/computeAFMutMatrix.html
+++ b/docs/reference/computeAFMutMatrix.html
@@ -1,50 +1,57 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>computeAFMutMatrix — computeAFMutMatrix • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="computeAFMutMatrix — computeAFMutMatrix"><meta name="description" content="Calculate the allele frequency per variant.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculate the allele frequency per variant.
 Source: https://github.com/petervangalen/MAESTER-2021
 We can get AF values greater than 1, which is due to uninformative reads.
 See: https://gatk.broadinstitute.org/hc/en-us/articles/360035532252-Allele-Depth-AD-is-lower-than-expected
 and https://github.com/caleblareau/mgatk/issues/1
-We simply set these values to 1, since that is the actual information we have in this case."><meta property="og:description" content="Calculate the allele frequency per variant.
+We simply set these values to 1, since that is the actual information we have in this case."><title>computeAFMutMatrix — computeAFMutMatrix • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="computeAFMutMatrix — computeAFMutMatrix"><meta property="og:description" content="Calculate the allele frequency per variant.
 Source: https://github.com/petervangalen/MAESTER-2021
 We can get AF values greater than 1, which is due to uninformative reads.
 See: https://gatk.broadinstitute.org/hc/en-us/articles/360035532252-Allele-Depth-AD-is-lower-than-expected
 and https://github.com/caleblareau/mgatk/issues/1
-We simply set these values to 1, since that is the actual information we have in this case."></head><body>
+We simply set these values to 1, since that is the actual information we have in this case."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
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+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
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-      <h1>computeAFMutMatrix</h1>
-
+      <img src="" class="logo" alt=""><h1>computeAFMutMatrix</h1>
+      
       <div class="d-none name"><code>computeAFMutMatrix.Rd</code></div>
     </div>
 
@@ -64,34 +71,32 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>The prefix of the chromosome.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/getAltMatrix.html b/docs/reference/getAltMatrix.html
index 3dabd6c..c17aa7a 100644
--- a/docs/reference/getAltMatrix.html
+++ b/docs/reference/getAltMatrix.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>getAltMatrix — getAltMatrix • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="getAltMatrix — getAltMatrix"><meta name="description" content="We get the alt values from the MAEGATK results.
-Source: https://github.com/petervangalen/MAESTER-2021"><meta property="og:description" content="We get the alt values from the MAEGATK results.
-Source: https://github.com/petervangalen/MAESTER-2021"></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We get the alt values from the MAEGATK results.
+Source: https://github.com/petervangalen/MAESTER-2021"><title>getAltMatrix — getAltMatrix • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="getAltMatrix — getAltMatrix"><meta property="og:description" content="We get the alt values from the MAEGATK results.
+Source: https://github.com/petervangalen/MAESTER-2021"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
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+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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-
-      <h1>getAltMatrix</h1>
-
+      <img src="" class="logo" alt=""><h1>getAltMatrix</h1>
+      
       <div class="d-none name"><code>getAltMatrix.Rd</code></div>
     </div>
 
@@ -52,38 +59,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se-object">SE_object<a class="anchor" aria-label="anchor" href="#arg-se-object"></a></dt>
+    <dl><dt>SE_object</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-letter">letter<a class="anchor" aria-label="anchor" href="#arg-letter"></a></dt>
+<dt>letter</dt>
 <dd><p>The base you want to use. Character.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>The chromosome prefix used.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/getMutMatrix.html b/docs/reference/getMutMatrix.html
index 0e470eb..ca2f5b4 100644
--- a/docs/reference/getMutMatrix.html
+++ b/docs/reference/getMutMatrix.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>getMutMatrix — getMutMatrix • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="getMutMatrix — getMutMatrix"><meta name="description" content="This function gets the allele frequency for a specific allele. It is used in computeAFMutMatrix.
-Source: https://github.com/petervangalen/MAESTER-2021"><meta property="og:description" content="This function gets the allele frequency for a specific allele. It is used in computeAFMutMatrix.
-Source: https://github.com/petervangalen/MAESTER-2021"></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function gets the allele frequency for a specific allele. It is used in computeAFMutMatrix.
+Source: https://github.com/petervangalen/MAESTER-2021"><title>getMutMatrix — getMutMatrix • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="getMutMatrix — getMutMatrix"><meta property="og:description" content="This function gets the allele frequency for a specific allele. It is used in computeAFMutMatrix.
+Source: https://github.com/petervangalen/MAESTER-2021"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
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-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
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-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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 </nav><div class="container template-reference-topic">
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-
-      <h1>getMutMatrix</h1>
-
+      <img src="" class="logo" alt=""><h1>getMutMatrix</h1>
+      
       <div class="d-none name"><code>getMutMatrix.Rd</code></div>
     </div>
 
@@ -52,46 +59,44 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-cov">cov<a class="anchor" aria-label="anchor" href="#arg-cov"></a></dt>
+<dt>cov</dt>
 <dd><p>The coverage matrix from MAEGATK/MGATK.</p></dd>
 
 
-<dt id="arg-letter">letter<a class="anchor" aria-label="anchor" href="#arg-letter"></a></dt>
+<dt>letter</dt>
 <dd><p>The base we are interested in.</p></dd>
 
 
-<dt id="arg-ref-allele">ref_allele<a class="anchor" aria-label="anchor" href="#arg-ref-allele"></a></dt>
+<dt>ref_allele</dt>
 <dd><p>Vector of reference alleles.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>The chromosome prefix used.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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diff --git a/docs/reference/getReadMatrix.html b/docs/reference/getReadMatrix.html
index b846f63..c96427c 100644
--- a/docs/reference/getReadMatrix.html
+++ b/docs/reference/getReadMatrix.html
@@ -1,40 +1,47 @@
 <!DOCTYPE html>
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+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
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-
-      <h1>Get the counts for a specific base over all positions.</h1>
-
+      <img src="" class="logo" alt=""><h1>Get the counts for a specific base over all positions.</h1>
+      
       <div class="d-none name"><code>getReadMatrix.Rd</code></div>
     </div>
 
@@ -49,38 +56,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se">SE<a class="anchor" aria-label="anchor" href="#arg-se"></a></dt>
+    <dl><dt>SE</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-letter">letter<a class="anchor" aria-label="anchor" href="#arg-letter"></a></dt>
+<dt>letter</dt>
 <dd><p>The base for which we want the counts.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>The chromosome name used as a prefix.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
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-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
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diff --git a/docs/reference/getRefMatrix.html b/docs/reference/getRefMatrix.html
index 5960f14..3a32a3c 100644
--- a/docs/reference/getRefMatrix.html
+++ b/docs/reference/getRefMatrix.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>getRefMatrix — getRefMatrix • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="getRefMatrix — getRefMatrix"><meta name="description" content="We get the reference values from the MAEGATK result.
-Source: https://github.com/petervangalen/MAESTER-2021"><meta property="og:description" content="We get the reference values from the MAEGATK result.
-Source: https://github.com/petervangalen/MAESTER-2021"></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="We get the reference values from the MAEGATK result.
+Source: https://github.com/petervangalen/MAESTER-2021"><title>getRefMatrix — getRefMatrix • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="getRefMatrix — getRefMatrix"><meta property="og:description" content="We get the reference values from the MAEGATK result.
+Source: https://github.com/petervangalen/MAESTER-2021"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
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+</li>
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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-
-      <h1>getRefMatrix</h1>
-
+      <img src="" class="logo" alt=""><h1>getRefMatrix</h1>
+      
       <div class="d-none name"><code>getRefMatrix.Rd</code></div>
     </div>
 
@@ -52,38 +59,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-se-object">SE_object<a class="anchor" aria-label="anchor" href="#arg-se-object"></a></dt>
+    <dl><dt>SE_object</dt>
 <dd><p>SummarizedExperiment object.</p></dd>
 
 
-<dt id="arg-letter">letter<a class="anchor" aria-label="anchor" href="#arg-letter"></a></dt>
+<dt>letter</dt>
 <dd><p>The base you are analysing. You get a matrix that shows which cells have how many reference reads for this letter.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>The chromosome prefix used.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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diff --git a/docs/reference/get_consensus.html b/docs/reference/get_consensus.html
index 092d400..922540e 100644
--- a/docs/reference/get_consensus.html
+++ b/docs/reference/get_consensus.html
@@ -1,42 +1,49 @@
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-I want to remove some packages if they are not needed. See below which package apperantly wasn't needed."><meta property="og:description" content="We get the consensus information for a specific matrix.
-I want to remove some packages if they are not needed. See below which package apperantly wasn't needed."></head><body>
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+I want to remove some packages if they are not needed. See below which package apperantly wasn't needed."><title>get_consensus — get_consensus • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="get_consensus — get_consensus"><meta property="og:description" content="We get the consensus information for a specific matrix.
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+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
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-
-      <h1>get_consensus</h1>
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+      <img src="" class="logo" alt=""><h1>get_consensus</h1>
+      
       <div class="d-none name"><code>get_consensus.Rd</code></div>
     </div>
 
@@ -52,42 +59,40 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-alt-base">alt_base<a class="anchor" aria-label="anchor" href="#arg-alt-base"></a></dt>
+    <dl><dt>alt_base</dt>
 <dd><p>The alternative base.</p></dd>
 
 
-<dt id="arg-ref-base">ref_base<a class="anchor" aria-label="anchor" href="#arg-ref-base"></a></dt>
+<dt>ref_base</dt>
 <dd><p>The reference base.</p></dd>
 
 
-<dt id="arg-input-matrix">input_matrix<a class="anchor" aria-label="anchor" href="#arg-input-matrix"></a></dt>
+<dt>input_matrix</dt>
 <dd><p>Input matrix with the present reads numerically encoded.</p></dd>
 
 
-<dt id="arg-chromosome-prefix">chromosome_prefix<a class="anchor" aria-label="anchor" href="#arg-chromosome-prefix"></a></dt>
+<dt>chromosome_prefix</dt>
 <dd><p>The chromosome name used as a prefix.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index 59c8a2d..5d85f5c 100644
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-      <h1>Package index</h1>
+      <img src="" class="logo" alt=""><h1>Function reference</h1>
     </div>
 
     <div class="section level2">
       <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="#all-functions"></a></h2>
+      
+      
 
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+      
+    </div><div id="" class="section level2">
+      
+      
+      
 
       <dl><dt>
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-          <code><a href="AllelFrequencyFoldChange.html">AllelFrequencyFoldChange()</a></code>
-
+          
+          <code><a href="AllelFrequencyFoldChange.html">AllelFrequencyFoldChange()</a></code> 
         </dt>
         <dd>AllelFrequencyFoldChange</dd>
       </dl><dl><dt>
-
-          <code><a href="AmpliconSupplementing.html">AmpliconSupplementing()</a></code>
-
+          
+          <code><a href="AmpliconSupplementing.html">AmpliconSupplementing()</a></code> 
         </dt>
         <dd>Supplementing scRNAseq values with Amplicon values</dd>
       </dl><dl><dt>
-
-          <code><a href="CalculateAlleleFrequency.html">CalculateAlleleFrequency()</a></code>
-
+          
+          <code><a href="CalculateAlleleFrequency.html">CalculateAlleleFrequency()</a></code> 
         </dt>
         <dd>Calculating the Minor Allele Frequency.</dd>
       </dl><dl><dt>
-
-          <code><a href="CalculateAltReads.html">CalculateAltReads()</a></code>
-
+          
+          <code><a href="CalculateAltReads.html">CalculateAltReads()</a></code> 
         </dt>
         <dd>CalculateAltReads</dd>
       </dl><dl><dt>
-
-          <code><a href="CalculateConsensus.html">CalculateConsensus()</a></code>
-
+          
+          <code><a href="CalculateConsensus.html">CalculateConsensus()</a></code> 
         </dt>
         <dd>CalculateConsensus</dd>
       </dl><dl><dt>
-
-          <code><a href="CalculateCorrelationPValue.html">CalculateCorrelationPValue()</a></code>
-
+          
+          <code><a href="CalculateCorrelationPValue.html">CalculateCorrelationPValue()</a></code> 
         </dt>
         <dd>Correlating the SNVs</dd>
       </dl><dl><dt>
-
-          <code><a href="CalculateCoverage.html">CalculateCoverage()</a></code>
-
+          
+          <code><a href="CalculateCoverage.html">CalculateCoverage()</a></code> 
         </dt>
         <dd>CalculateCoverage</dd>
       </dl><dl><dt>
-
-          <code><a href="CalculateFisherTestPValue.html">CalculateFisherTestPValue()</a></code>
-
+          
+          <code><a href="CalculateFisherTestPValue.html">CalculateFisherTestPValue()</a></code> 
         </dt>
         <dd>CalculateFisherTestPValue</dd>
       </dl><dl><dt>
-
-          <code><a href="CalculateQuality.html">CalculateQuality()</a></code>
-
+          
+          <code><a href="CalculateQuality.html">CalculateQuality()</a></code> 
         </dt>
         <dd>CalculateQuality</dd>
       </dl><dl><dt>
-
-          <code><a href="CalculateRefReads.html">CalculateRefReads()</a></code>
-
+          
+          <code><a href="CalculateRefReads.html">CalculateRefReads()</a></code> 
         </dt>
         <dd>CalculateRefReads</dd>
       </dl><dl><dt>
-
-          <code><a href="CalculateStrandCorrelation.html">CalculateStrandCorrelation()</a></code>
-
+          
+          <code><a href="CalculateStrandCorrelation.html">CalculateStrandCorrelation()</a></code> 
         </dt>
         <dd>CalculateStrandCorrelation</dd>
       </dl><dl><dt>
-
-          <code><a href="CallSupport.html">CallSupport()</a></code>
-
+          
+          <code><a href="CallSupport.html">CallSupport()</a></code> 
         </dt>
         <dd>CallSupport</dd>
       </dl><dl><dt>
-
-          <code><a href="ClonalDefinition.html">ClonalDefinition()</a></code>
-
+          
+          <code><a href="ClonalDefinition.html">ClonalDefinition()</a></code> 
         </dt>
         <dd>Defining clones.</dd>
       </dl><dl><dt>
-
-          <code><a href="ClonalDiversity.html">ClonalDiversity()</a></code>
-
+          
+          <code><a href="ClonalDiversity.html">ClonalDiversity()</a></code> 
         </dt>
         <dd>Determining the clonal diversity.</dd>
       </dl><dl><dt>
-
-          <code><a href="CombineSEobjects.html">CombineSEobjects()</a></code>
-
+          
+          <code><a href="CombineSEobjects.html">CombineSEobjects()</a></code> 
         </dt>
         <dd>CombineSEobjects</dd>
       </dl><dl><dt>
-
-          <code><a href="Enrichment_FisherTest.html">Enrichment_FisherTest()</a></code>
-
+          
+          <code><a href="Enrichment_FisherTest.html">Enrichment_FisherTest()</a></code> 
         </dt>
         <dd>Enrichment_FisherTest</dd>
       </dl><dl><dt>
-
-          <code><a href="Filtering.html">Filtering()</a></code>
-
+          
+          <code><a href="Filtering.html">Filtering()</a></code> 
         </dt>
         <dd>Filtering the loaded genotyping data.</dd>
       </dl><dl><dt>
-
-          <code><a href="GetCellInfoPerVariant.html">GetCellInfoPerVariant()</a></code>
-
+          
+          <code><a href="GetCellInfoPerVariant.html">GetCellInfoPerVariant()</a></code> 
         </dt>
         <dd>We get the variant information per cell.</dd>
       </dl><dl><dt>
-
-          <code><a href="GetVariantInfo.html">GetVariantInfo()</a></code>
-
+          
+          <code><a href="GetVariantInfo.html">GetVariantInfo()</a></code> 
         </dt>
         <dd>GetVariantInfo</dd>
       </dl><dl><dt>
-
-          <code><a href="HeatmapVoi.html">HeatmapVoi()</a></code>
-
+          
+          <code><a href="HeatmapVoi.html">HeatmapVoi()</a></code> 
         </dt>
         <dd>HeatmapVoi</dd>
       </dl><dl><dt>
-
-          <code><a href="LoadingMAEGATK_typewise.html">LoadingMAEGATK_typewise()</a></code>
-
+          
+          <code><a href="LoadingMAEGATK_typewise.html">LoadingMAEGATK_typewise()</a></code> 
         </dt>
         <dd>LoadingMAEGATK_typewise</dd>
       </dl><dl><dt>
-
-          <code><a href="LoadingRawMatrix_typewise.html">LoadingRawMatrix_typewise()</a></code>
-
+          
+          <code><a href="LoadingRawMatrix_typewise.html">LoadingRawMatrix_typewise()</a></code> 
         </dt>
         <dd>LoadingRawMatrix_typewise</dd>
       </dl><dl><dt>
-
-          <code><a href="LoadingVCF_typewise.html">LoadingVCF_typewise()</a></code>
-
+          
+          <code><a href="LoadingVCF_typewise.html">LoadingVCF_typewise()</a></code> 
         </dt>
         <dd>LoadingVCF_typewise</dd>
       </dl><dl><dt>
-
-          <code><a href="LoadingVarTrix_typewise.html">LoadingVarTrix_typewise()</a></code>
-
+          
+          <code><a href="LoadingVarTrix_typewise.html">LoadingVarTrix_typewise()</a></code> 
         </dt>
         <dd>LoadingVarTrix_typewise</dd>
       </dl><dl><dt>
-
-          <code><a href="Merging_SE_list.html">Merging_SE_list()</a></code>
-
+          
+          <code><a href="Merging_SE_list.html">Merging_SE_list()</a></code> 
         </dt>
         <dd>Merging list of SummarizedExperiment objects.</dd>
       </dl><dl><dt>
-
-          <code><a href="RowWiseSplit.html">RowWiseSplit()</a></code>
-
+          
+          <code><a href="RowWiseSplit.html">RowWiseSplit()</a></code> 
         </dt>
         <dd>RowWiseSplit</dd>
       </dl><dl><dt>
-
-          <code><a href="SeparatingMatrixToList.html">SeparatingMatrixToList()</a></code>
-
+          
+          <code><a href="SeparatingMatrixToList.html">SeparatingMatrixToList()</a></code> 
         </dt>
         <dd>SeparatingMatrixToList</dd>
       </dl><dl><dt>
-
-          <code><a href="SetVariantInfo.html">SetVariantInfo()</a></code>
-
+          
+          <code><a href="SetVariantInfo.html">SetVariantInfo()</a></code> 
         </dt>
         <dd>SetVariantInfo</dd>
       </dl><dl><dt>
-
-          <code><a href="UMIQC.html">UMIQC()</a></code>
-
+          
+          <code><a href="UMIQC.html">UMIQC()</a></code> 
         </dt>
         <dd>UMIQC</dd>
       </dl><dl><dt>
-
-          <code><a href="UMI_seq.html">UMI_seq()</a></code>
-
+          
+          <code><a href="UMI_seq.html">UMI_seq()</a></code> 
         </dt>
         <dd>UMI_seq</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantBurden.html">VariantBurden()</a></code>
-
+          
+          <code><a href="VariantBurden.html">VariantBurden()</a></code> 
         </dt>
         <dd>VariantBurden</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantCloneSizeThresholding.html">VariantCloneSizeThresholding()</a></code>
-
+          
+          <code><a href="VariantCloneSizeThresholding.html">VariantCloneSizeThresholding()</a></code> 
         </dt>
         <dd>VariantCloneSizeThresholding</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantCorrelationHeatmap.html">VariantCorrelationHeatmap()</a></code>
-
+          
+          <code><a href="VariantCorrelationHeatmap.html">VariantCorrelationHeatmap()</a></code> 
         </dt>
         <dd>VariantCorrelationHeatmap</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantFisherTestHeatmap.html">VariantFisherTestHeatmap()</a></code>
-
+          
+          <code><a href="VariantFisherTestHeatmap.html">VariantFisherTestHeatmap()</a></code> 
         </dt>
         <dd>VariantFisherTestHeatmap</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantQuantileThresholding_Combined.html">VariantQuantileThresholding_Combined()</a></code>
-
+          
+          <code><a href="VariantQuantileThresholding_Combined.html">VariantQuantileThresholding_Combined()</a></code> 
         </dt>
         <dd>VariantQuantileThresholding_Combined</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantSelection_Group.html">VariantSelection_Group()</a></code>
-
+          
+          <code><a href="VariantSelection_Group.html">VariantSelection_Group()</a></code> 
         </dt>
         <dd>VariantSelection_Group</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantSelection_Quantile.html">VariantSelection_Quantile()</a></code>
-
+          
+          <code><a href="VariantSelection_Quantile.html">VariantSelection_Quantile()</a></code> 
         </dt>
         <dd>VariantSelection_Quantile</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantSelection_TopCells.html">VariantSelection_TopCells()</a></code>
-
+          
+          <code><a href="VariantSelection_TopCells.html">VariantSelection_TopCells()</a></code> 
         </dt>
         <dd>VariantSelection_TopCells</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantWiseCorrelation.html">VariantWiseCorrelation()</a></code>
-
+          
+          <code><a href="VariantWiseCorrelation.html">VariantWiseCorrelation()</a></code> 
         </dt>
         <dd>VariantWiseCorrelation</dd>
       </dl><dl><dt>
-
-          <code><a href="VariantWiseFisherTest.html">VariantWiseFisherTest()</a></code>
-
+          
+          <code><a href="VariantWiseFisherTest.html">VariantWiseFisherTest()</a></code> 
         </dt>
         <dd>VariantWiseFisherTest</dd>
       </dl><dl><dt>
-
-          <code><a href="char_to_numeric.html">char_to_numeric()</a></code>
-
+          
+          <code><a href="char_to_numeric.html">char_to_numeric()</a></code> 
         </dt>
         <dd>char_to_numeric</dd>
       </dl><dl><dt>
-
-          <code><a href="combine_NAMES.html">combine_NAMES()</a></code>
-
+          
+          <code><a href="combine_NAMES.html">combine_NAMES()</a></code> 
         </dt>
         <dd>combine_NAMES</dd>
       </dl><dl><dt>
-
-          <code><a href="combine_SparseMatrix.html">combine_SparseMatrix()</a></code>
-
+          
+          <code><a href="combine_SparseMatrix.html">combine_SparseMatrix()</a></code> 
         </dt>
         <dd>combine_sparseMatrix</dd>
       </dl><dl><dt>
-
-          <code><a href="computeAFMutMatrix.html">computeAFMutMatrix()</a></code>
-
+          
+          <code><a href="computeAFMutMatrix.html">computeAFMutMatrix()</a></code> 
         </dt>
         <dd>computeAFMutMatrix</dd>
       </dl><dl><dt>
-
-          <code><a href="getAltMatrix.html">getAltMatrix()</a></code>
-
+          
+          <code><a href="getAltMatrix.html">getAltMatrix()</a></code> 
         </dt>
         <dd>getAltMatrix</dd>
       </dl><dl><dt>
-
-          <code><a href="getMutMatrix.html">getMutMatrix()</a></code>
-
+          
+          <code><a href="getMutMatrix.html">getMutMatrix()</a></code> 
         </dt>
         <dd>getMutMatrix</dd>
       </dl><dl><dt>
-
-          <code><a href="getReadMatrix.html">getReadMatrix()</a></code>
-
+          
+          <code><a href="getReadMatrix.html">getReadMatrix()</a></code> 
         </dt>
         <dd>Get the counts for a specific base over all positions.</dd>
       </dl><dl><dt>
-
-          <code><a href="getRefMatrix.html">getRefMatrix()</a></code>
-
+          
+          <code><a href="getRefMatrix.html">getRefMatrix()</a></code> 
         </dt>
         <dd>getRefMatrix</dd>
       </dl><dl><dt>
-
-          <code><a href="get_consensus.html">get_consensus()</a></code>
-
+          
+          <code><a href="get_consensus.html">get_consensus()</a></code> 
         </dt>
         <dd>get_consensus</dd>
       </dl><dl><dt>
-
-          <code><a href="load_object.html">load_object()</a></code>
-
+          
+          <code><a href="load_object.html">load_object()</a></code> 
         </dt>
         <dd>load_object</dd>
       </dl><dl><dt>
-
-          <code><a href="save_object.html">save_object()</a></code>
-
+          
+          <code><a href="save_object.html">save_object()</a></code> 
         </dt>
         <dd>save_object</dd>
       </dl><dl><dt>
-
-          <code><a href="sdiv.html">sdiv()</a></code>
-
+          
+          <code><a href="sdiv.html">sdiv()</a></code> 
         </dt>
         <dd>Division of sparse matrix.</dd>
       </dl></div>
@@ -364,18 +319,18 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
-
+  
 
   </body></html>
 
diff --git a/docs/reference/load_object.html b/docs/reference/load_object.html
index b84126a..33c57c1 100644
--- a/docs/reference/load_object.html
+++ b/docs/reference/load_object.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>load_object — load_object • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="load_object — load_object"><meta name="description" content="A loading function to load the RDS files quicker.
-Source: https://github.com/CostaLab/CimpleG"><meta property="og:description" content="A loading function to load the RDS files quicker.
-Source: https://github.com/CostaLab/CimpleG"></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A loading function to load the RDS files quicker.
+Source: https://github.com/CostaLab/CimpleG"><title>load_object — load_object • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="load_object — load_object"><meta property="og:description" content="A loading function to load the RDS files quicker.
+Source: https://github.com/CostaLab/CimpleG"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
 
-
-    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.1</small>
 
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+    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
 <li class="nav-item dropdown">
-  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a></li>
-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
-    <li><a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
-      </ul></div>
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
+      <ul class="navbar-nav"></ul></div>
 
+    
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>load_object</h1>
-
+      <img src="" class="logo" alt=""><h1>load_object</h1>
+      
       <div class="d-none name"><code>load_object.Rd</code></div>
     </div>
 
@@ -52,30 +59,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-file-name">file_name<a class="anchor" aria-label="anchor" href="#arg-file-name"></a></dt>
+    <dl><dt>file_name</dt>
 <dd><p>The path to the file.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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+  
 
-
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diff --git a/docs/reference/save_object.html b/docs/reference/save_object.html
index 30ffbd4..c805cd9 100644
--- a/docs/reference/save_object.html
+++ b/docs/reference/save_object.html
@@ -1,42 +1,49 @@
 <!DOCTYPE html>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Saving function to save the RDS files quicker.
+Source:https://github.com/CostaLab/CimpleG"><title>save_object — save_object • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="save_object — save_object"><meta property="og:description" content="Saving function to save the RDS files quicker.
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+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
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-      <h1>save_object</h1>
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+      <img src="" class="logo" alt=""><h1>save_object</h1>
+      
       <div class="d-none name"><code>save_object.Rd</code></div>
     </div>
 
@@ -52,38 +59,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
+    <dl><dt>object</dt>
 <dd><p>The R object to be save.</p></dd>
 
 
-<dt id="arg-file-name">file_name<a class="anchor" aria-label="anchor" href="#arg-file-name"></a></dt>
+<dt>file_name</dt>
 <dd><p>The path were the file shall be save.</p></dd>
 
 
-<dt id="arg-file-format">file_format<a class="anchor" aria-label="anchor" href="#arg-file-format"></a></dt>
+<dt>file_format</dt>
 <dd><p>The format of the save file. Has to be one of: zstd, lz4, gzip, bzip2, xz, nocomp.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
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diff --git a/docs/reference/sdiv.html b/docs/reference/sdiv.html
index 2dbec76..3b650ba 100644
--- a/docs/reference/sdiv.html
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 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Division of sparse matrix. — sdiv • sigurd</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Division of sparse matrix. — sdiv"><meta name="description" content="Division of sparse matrix."><meta property="og:description" content="Division of sparse matrix."></head><body>
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     <a class="navbar-brand me-2" href="../index.html">sigurd</a>
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item">
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-    <li><a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a></li>
-    <li><a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a></li>
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+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/BoneMarrow_SIGURD.html">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</a>
+    <a class="dropdown-item" href="../articles/MPN_SIGURD.html">MPN SIGURD</a>
+    <a class="dropdown-item" href="../articles/SW_CellMixture_SIGURD.html">Cell Mixture Analysis using Seq-Well Sequencing</a>
+    <a class="dropdown-item" href="../articles/TenX_CellMixture_SIGURD.html">Cell Mixture Experiment using 10X Genomics Sequencing</a>
+  </div>
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+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-
-      <h1>Division of sparse matrix.</h1>
-
+      <img src="" class="logo" alt=""><h1>Division of sparse matrix.</h1>
+      
       <div class="d-none name"><code>sdiv.Rd</code></div>
     </div>
 
@@ -49,38 +56,36 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-
-
-<dl><dt id="arg-x">X<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+    <dl><dt>X</dt>
 <dd><p>First sparse matrix.</p></dd>
 
 
-<dt id="arg-y">Y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt>Y</dt>
 <dd><p>Second sparse matrix.</p></dd>
 
 
-<dt id="arg-names">names<a class="anchor" aria-label="anchor" href="#arg-names"></a></dt>
+<dt>names</dt>
 <dd><p>The dimension names (dimnames(X)).</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Martin Grasshoff, Ivan Costa.</p>
+  <p></p><p>Developed by Martin Grasshoff, Ivan Costa.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
 
+  
 
-
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+  
 
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diff --git a/docs/search.json b/docs/search.json
index 210908c..a8f647d 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"analysis-of-blastic-plasmacytoid-dendritic-cell-neoplasm-bpdcn","dir":"Articles","previous_headings":"","what":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":", compare analysis cells patient BPDCN. original script available : https://github.com/petervangalen/MAESTER-2021/blob/main/4_CH_sample/4.2_Variant_Selection.R setup, cells single donor separated categories. small clones might characterize clonal lineages sample selected.","code":""},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"loading-necessary-packages-","dir":"Articles","previous_headings":"","what":"Loading necessary packages.","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"load data MAESTER.","code":"print(\"Libraries for SIGURD.\") ## [1] \"Libraries for SIGURD.\" suppressPackageStartupMessages(library(sigurd)) suppressPackageStartupMessages(library(SummarizedExperiment)) suppressPackageStartupMessages(library(ggplot2))"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"loading-the-data-using-sigurd-","dir":"Articles","previous_headings":"","what":"Loading the data using SIGURD.","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"","code":"# The design matrix contains information for the genotyping data. genotyping <- LoadingMAEGATK_typewise(patient = \"BPDCN712\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv\", type_use = \"Amplicon_MT\", verbose = FALSE)  # Loading the scRNA-seq data. scrna <- readRDS(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/BPDCN712_Seurat_with_TCR_Renamed.rds\")"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"generating-a-block-list","dir":"Articles","previous_headings":"","what":"Generating a block list","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"Variants also detected cell mixture data treated possible false positives. used blacklist removed results.","code":"# Loading the TenX Cell Mixture Genotyping.  genotyping_tenx <- load_object(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/TenX_CellMixture_Genotyping.rds.lz4\") blocklist <- AllelFrequencyFoldChange(genotyping_tenx, group_of_interest = \"CellType\", group1 = \"K562\", group2 = \"BT142\", maximum_foldchange = 5, minimum_coverage = 5, minimum_allele_freq = 0.001, maximum_allele_freq = 0.999)$Variant  # We add the variant chrM_1583_A_G by hand. It is identified as misleading based on downstream analysis. blocklist <- c(blocklist, \"chrM_1583_A_G\")"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"selecting-the-variants-of-interest","dir":"Articles","previous_headings":"","what":"Selecting the Variants of Interest","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"Now, select variants interest loaded data.","code":"voi.ch.sigurd <- VariantSelection_TopCells(genotyping, min_coverage = 5, quantiles = 0.9, thresholds = 0, top_cells = 10, top_VAF = 0.5, min_quality = 30, remove_nocall = FALSE, verbose = FALSE) voi.ch.sigurd <- voi.ch.sigurd[!voi.ch.sigurd %in% blocklist] print(voi.ch.sigurd) ##  [1] \"chrM_683_G_A\"   \"chrM_1323_G_A\"  \"chrM_1415_G_A\"  \"chrM_2593_G_A\"  ##  [5] \"chrM_6205_G_A\"  \"chrM_6243_G_A\"  \"chrM_8697_G_A\"  \"chrM_9753_G_A\"  ##  [9] \"chrM_10158_T_A\" \"chrM_15140_G_A\" \"chrM_15812_G_A\" \"chrM_779_T_C\"   ## [13] \"chrM_3988_T_C\"  \"chrM_6185_T_C\"  \"chrM_6293_T_C\"  \"chrM_9164_T_C\"  ## [17] \"chrM_9321_T_C\"  \"chrM_11864_T_C\" \"chrM_15299_T_C\" \"chrM_1171_A_G\"  ## [21] \"chrM_1222_A_G\"  \"chrM_2241_A_G\"  \"chrM_2623_A_G\"  \"chrM_3628_A_G\"  ## [25] \"chrM_4104_A_G\"  \"chrM_6218_A_G\""},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"visualisation-using-sigurd","dir":"Articles","previous_headings":"","what":"Visualisation using SIGURD","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"","code":"genotyping <- Filtering(SE = genotyping, cells_include = colnames(scrna)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" colData(genotyping)$CellType <- scrna$CellType HeatmapVoi(SE = genotyping, voi = voi.ch.sigurd, annotation_trait = \"CellType\", sort_cells = TRUE, remove_empty_cells = TRUE, minimum_allele_freq = 0.01)"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"cell-type-enrichment-2593ga","dir":"Articles","previous_headings":"","what":"Cell Type Enrichment 2593G>A","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"check cell type enrichment variant 2593G>.","code":"result_enrichment <- Enrichment_FisherTest(se = genotyping, variant = \"chrM_2593_G_A\", use_nocall = FALSE, trait = \"CellType\") ## [1] \"We get a count matrix of the chrM_2593_G_A per CellType.\" ComplexHeatmap::Heatmap(as.matrix(result_enrichment$Heatmap_Values), cluster_rows = FALSE, cluster_columns = FALSE, col= circlize::colorRamp2(c(0, max(result_enrichment$Heatmap_Values, na.rm = TRUE)), c(\"white\", \"red\")))"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"cell-type-enrichment-6243ga","dir":"Articles","previous_headings":"","what":"Cell Type Enrichment 6243G>A","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"check cell type enrichment variant 6243G>.","code":"result_enrichment <- Enrichment_FisherTest(se = genotyping, variant = \"chrM_6243_G_A\", use_nocall = FALSE, trait = \"CellType\") ## [1] \"We get a count matrix of the chrM_6243_G_A per CellType.\" ComplexHeatmap::Heatmap(as.matrix(result_enrichment$Heatmap_Values), cluster_rows = FALSE, cluster_columns = FALSE, col= circlize::colorRamp2(c(0, max(result_enrichment$Heatmap_Values, na.rm = TRUE)), c(\"white\", \"red\")))"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"enrichment-with-somatic-variants","dir":"Articles","previous_headings":"","what":"Enrichment with somatic variants","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"get number 2593_G>cells also mutated different somatic variant.","code":"somatic_variants <- c(\"ASXL1.G642fs.1\", \"ASXL1.G642fs.2\", \"TET2.S792X\", \"TET2.Q1034X\", \"TET2.R1216X\", \"TET2.H1380Y\") variants <- LoadingRawMatrix_typewise(samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv\", patient = \"BPDCN712\", variant_use = somatic_variants, matrix_column_separator = \"\\t\", verbose = FALSE) genotyping <- genotyping[voi.ch.sigurd, ] genotyping <- Filtering(genotyping, cells_include = colnames(variants)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" variants <- Filtering(variants, cells_include = colnames(scrna), fraction_threshold = 0.01, reject_value = \"Reference\") ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We assume that cells with a fraction smaller than our threshold are actually Reference.\" ## [1] \"We set consensus values to 1 (Reference) and fraction values to 0.\" ## [1] \"We do not set fractions between 0.01 and 1 to 1.\" ## [1] \"This way, we retain the heterozygous information.\" ## [1] \"We remove all the variants that are always NoCall.\" genotyping <- CombineSEobjects(se_1 = genotyping, se_2 = variants) genotyping <- ClonalDefinition(se = genotyping, variants_ls = list(\"chrM_2593_G_A\"), grouping = NULL, identities = NULL, explicit = TRUE, explicit_not = list(\"chrM_6243_G_A\"), explicit_min_vaf = 0.01, verbose = TRUE) ## [1] \"Explicit clone definition.\" genotyping <- genotyping[, genotyping$Clones == \"C1\"] res <- VariantWiseFisherTest(variants_list = RowWiseSplit(se = genotyping)) ## [1] \"Testing Variant: ASXL1.G642fs.1, 1 out of 6\" ## [1] \"Testing Variant: ASXL1.G642fs.2, 2 out of 6\" ## [1] \"Testing Variant: TET2.S792X, 3 out of 6\" ## [1] \"Testing Variant: TET2.Q1034X, 4 out of 6\" ## [1] \"Testing Variant: TET2.R1216X, 5 out of 6\" ## [1] \"Testing Variant: TET2.H1380Y, 6 out of 6\" ## [1] \"We remove the NA P values.\" ## [1] \"Adjusting P values using fdr.\" knitr::kable(res, format=\"html\")"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"loading-necessary-packages-","dir":"Articles","previous_headings":"","what":"Loading necessary packages.","title":"MPN SIGURD","text":"","code":"suppressPackageStartupMessages(library(sigurd)) suppressPackageStartupMessages(library(SummarizedExperiment)) suppressPackageStartupMessages(library(ggplot2)) suppressPackageStartupMessages(library(Seurat)) suppressPackageStartupMessages(library(ComplexHeatmap)) suppressPackageStartupMessages(library(circlize)) suppressPackageStartupMessages(library(grid)) suppressPackageStartupMessages(library(EnhancedVolcano))"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"analysis-of-mpn-data","dir":"Articles","previous_headings":"","what":"Analysis of MPN data","title":"MPN SIGURD","text":", illustrate analysis genotyping data MPN samples. JAK2V617F mutation genotyped 6 MPN samples 3 healthy controls. setup makes analysis different previous analyses. Previously, one sample analysed time. Now, load analyse samples simultaneously.","code":""},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"loading-mpn-data","dir":"Articles","previous_headings":"","what":"Loading MPN data","title":"MPN SIGURD","text":"Now, load JAK2V617F data plot mutated cells UMAP. Since loading multiple samples, code complicated code MAESTER SW sample.","code":"# Loading the scRNA-seq data. scrna <- load_object(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/scrna_MPN.rds.lz4\")  # Loading the genotyping data. genotyping  <- LoadingVarTrix_typewise(patient = \"MPN\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_VarTrix.csv\", min_reads = 0, vcf_path = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/CosmicSubset_JAK2V617F.vcf\", type_use = \"scRNAseq_Somatic\", min_cells = 0, verbose = FALSE) amplicon <- LoadingVarTrix_typewise(patient = \"MPN\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_Amplicon.csv\", min_reads = 0, vcf_path = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/CosmicSubset_UCSC_JAK2V617F.vcf\", type_use = \"scRNAseq_Amplicon\", min_cells = 0, verbose = FALSE) genotyping  <- AmpliconSupplementing(scRNAseq = genotyping, amplicon = amplicon, verbose = FALSE)  # Filtering the genotyping object to remove false positives. genotyping <- Filtering(genotyping, min_cells_per_variant = 0, fraction_threshold = 0.21, cells_include = colnames(scrna), min_variants_per_cell = 1, reject_value = \"NoCall\", verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"combining-seurat-and-sigurd","dir":"Articles","previous_headings":"","what":"Combining Seurat and SIGURD","title":"MPN SIGURD","text":"Now, add genotyping information Seurat object.","code":"scrna <- SetVariantInfo(SE = genotyping, seurat_object = scrna) ## [1] \"You did not supply a vector of variants. All variants will be used.\""},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"visualisation","dir":"Articles","previous_headings":"","what":"Visualisation","title":"MPN SIGURD","text":"visualise genotyping information UMAP.","code":"# Plotting the mutated cells on the UMAP. scrna$JAK2_p.V617F_c.1849G.T_consensus <- factor(scrna$JAK2_p.V617F_c.1849G.T_consensus, levels = c(\"Ref\", \"Alt\")) jak2_cells <- sum(scrna$JAK2_p.V617F_c.1849G.T_consensus == \"Alt\", na.rm = TRUE) ref_cells <- sum(scrna$JAK2_p.V617F_c.1849G.T_consensus == \"Ref\", na.rm = TRUE) all_cells <- ncol(scrna) p <- DimPlot(scrna, group.by = \"JAK2_p.V617F_c.1849G.T_consensus\", reduction = \"INTE_UMAP\", order = TRUE, pt.size = 1, raster = FALSE, na.value = \"grey95\", cols = c(Alt = \"#aa0051\", Ref = \"#79b938\")) +   ggtitle(paste0(\"Alt: \", jak2_cells, \", Ref: \", ref_cells, \", All: \", all_cells)) +   xlab(\"UMAP 1\") + ylab(\"UMAP 2\") + scale_color_manual(breaks = c(\"Alt\", \"Ref\"), values = c(\"#aa0051\", \"#79b938\"), na.value = \"grey95\") +   theme(legend.position = \"top\") ## Scale for colour is already present. ## Adding another scale for colour, which will replace the existing scale. print(p)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"we-determine-degs-between-the-jak2v617f-and-wt-cells-","dir":"Articles","previous_headings":"","what":"We determine DEGs between the JAK2V617F and WT cells.","title":"MPN SIGURD","text":"Now, determine DEGs JAK2V617F cells wild type cells Orthochromatic Erythroblasts.","code":"scrna_orthoe <- subset(scrna, CellType == \"Orthochromatic Erythroblasts\" & Condition != \"HC\") degs <- FindMarkers(scrna_orthoe, group.by = \"JAK2_p.V617F_c.1849G.T_consensus\", ident.1 = \"Alt\", ident.2 = \"Ref\", logfc.threshold = 0) degs <- data.frame(degs, gene = rownames(degs)) degs_up   <- nrow(subset(degs, avg_log2FC >   0.25 & p_val_adj < 0.05)) degs_down <- nrow(subset(degs, avg_log2FC <  -0.25 & p_val_adj < 0.05)) EnhancedVolcano(degs, x = \"avg_log2FC\", y = \"p_val_adj\", lab = degs$gene, FCcutoff = 0.25, pCutoff = 0.05, title = \"OrthoE JAK2V617F Pos. vs. Neg.\",subtitle = NULL)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"combining-the-jak2v617f-data-with-the-mt-data-","dir":"Articles","previous_headings":"","what":"Combining the JAK2V617F data with the MT data.","title":"MPN SIGURD","text":"combine JAK2V617F SIGURD object MT object. Cells variants objects combined. save time, processing single sample. samples processed equally. Since genotyping object list, easily processed using parallel computing. First, load filter mitochondrial variant information.","code":"# Loading the data.  genotyping_mt <- LoadingMAEGATK_typewise(patient = \"MPN1\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_MT.csv\", min_cells = 0, cells_include = colnames(scrna), type_use = \"scRNAseq_MT\", verbose = FALSE) genotyping_mt <- Filtering(genotyping_mt, min_variants_per_cell = 1, min_cells_per_variant = 2, fraction_threshold = 0.05, cells_include = colnames(scrna), verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"mpn-vois-and-diversity","dir":"Articles","previous_headings":"","what":"MPN VOIs and Diversity","title":"MPN SIGURD","text":"Now, select mtVOIs. determine clonal lineages plot results heatmap. subset cells include erythroid cells.","code":"# Subset to erythroid cells. erythroid_cells <- subset(scrna, annotation == \"ErythroidCells\") genotyping_mt <- Filtering(genotyping_mt, cells_include = colnames(erythroid_cells)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" # Selecting the mtVOIS. mt_vois <- VariantSelection_Quantile(genotyping_mt, min_coverage = 1, verbose = FALSE)  # Determining the clonal lineages. genotyping_mt <- ClonalDefinition(se = genotyping_mt, variants_ls = list(mt_vois), verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"visualisation-of-mtvois-and-clonal-lineages","dir":"Articles","previous_headings":"","what":"Visualisation of mtVOIs and Clonal Lineages","title":"MPN SIGURD","text":"now plot variants interest clonal lineages.","code":"# Generating a heatmap. colors_lineage <- c(\"C1\" = \"#563e00\", \"C2\" = \"#dec234\", \"C3\" = \"#e23856\", \"C4\" = \"#7f0073\", \"C5\" = \"#006639\", \"C6\" = \"#b1db8e\", \"C7\" = \"#00348f\", \"Negative\" = \"black\") ha <- columnAnnotation(Clones = colData(genotyping_mt)[,\"Clones\"],                        col = list(Clones = colors_lineage),                        annotation_name_gp = gpar(fontsize = 10, fontface = \"plain\"),                        annotation_legend_param = list(Clones = list(nrow = 1, title = \"\"))) fraction <- as.matrix(assays(genotyping_mt)[[\"fraction\"]])[mt_vois, ] hm <- Heatmap(fraction,   name = \"VAF\",   row_title_gp = gpar(fontsize = 12),   row_names_gp = gpar(fontsize = 10),   row_names_max_width = unit(16, \"cm\"),   column_title = \"MPN1\",   column_title_gp = gpar(fontsize = 12),   column_names_gp = gpar(fontsize = 10),   col = colorRamp2(seq(0, round(max(fraction, na.rm = TRUE)), length.out = 9), c(\"#FCFCFC\", \"#FFEDB0\", \"#FFDF5F\", \"#FEC510\", \"#FA8E24\", \"#F14C2B\", \"#DA2828\", \"#BE2222\", \"#A31D1D\")),   show_column_dend = FALSE,   show_row_names = TRUE,   show_column_names = FALSE,   cluster_columns = TRUE,   cluster_rows = FALSE,   heatmap_legend_param = list(border = \"#000000\", grid_height = unit(10, \"mm\"),   direction = \"horizontal\"),   bottom_annotation = ha,   border = TRUE,   use_raster = TRUE,   show_heatmap_legend = TRUE) draw(hm, annotation_legend_side = \"bottom\")"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"calculating-clonal-diversity-","dir":"Articles","previous_headings":"","what":"Calculating clonal diversity.","title":"MPN SIGURD","text":"calculate clonal diversity sample MPN1 example.","code":"clonal_diversity <- ClonalDiversity(genotyping_mt, grouping = \"Clones\", diversity_measure = \"EffectiveSpecies\", verbose = FALSE) print(paste0(\"Clonal Diversity in Effective Number of Species for MPN1: \", clonal_diversity)) ## [1] \"Clonal Diversity in Effective Number of Species for MPN1: 6.72545022391521\""},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"repeating-the-mt-analysis-for-all-samples-","dir":"Articles","previous_headings":"","what":"Repeating the MT analysis for all samples.","title":"MPN SIGURD","text":"now repeat MT analysis samples. take considereable time. speed analsyis using parallel computing. load results generated code.","code":"# We get all patients present in the design matrix. design_matrix <- read.table(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_MT.csv\", header = TRUE, sep = \",\") patients <- design_matrix$patient[1] genotyping_mt_all <- parallel::mclapply(patients, LoadingMAEGATK_typewise, samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_MT.csv\", min_cells = 0, cells_include = colnames(scrna), type_use = \"scRNAseq_MT\", verbose = FALSE, mc.cores = length(patients)) names(genotyping_mt_all) <- patients genotyping_mt_all <- parallel::mclapply(genotyping_mt_all, Filtering, min_variants_per_cell = 1, min_cells_per_variant = 2, fraction_threshold = 0.05, cells_include = colnames(scrna), verbose = FALSE, mc.cores = length(patients))"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"selecting-variants-of-interest-for-all-samples","dir":"Articles","previous_headings":"","what":"Selecting variants of interest for all samples","title":"MPN SIGURD","text":"select variants interest samples.","code":"# Selecting the mtVOIS. mt_vois_all <- parallel::mclapply(genotyping_mt_all, VariantSelection_Quantile, min_coverage = 1, verbose = FALSE, mc.cores = length(patients))  # Determining the clonal lineages. This takes very long. We use parallel computing to process all samples simultaneously. genotyping_mt_all <- parallel::mclapply(1:length(mt_vois_all), function(x){   sample_use <- names(mt_vois_all)[x]   clones <- sigurd::ClonalDefinition(se = genotyping_mt_all[[sample_use]], mt_vois_all[sample_use], verbose = FALSE)   return(clones) }, mc.cores = length(mt_vois_all)) names(genotyping_mt_all) <- patients save_object(genotyping_mt_all, \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/genotyping_mt_all.rds.lz4\", \"lz4\")"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"calculating-the-diverstiy-for-all-samples","dir":"Articles","previous_headings":"","what":"Calculating the diverstiy for all samples","title":"MPN SIGURD","text":"","code":"# We load the previous results. genotyping_mt_all <- load_object(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/genotyping_mt_all.rds.lz4\") clonal_diversity_all <- unlist(lapply(genotyping_mt_all, ClonalDiversity, grouping = \"Clones\", diversity_measure = \"EffectiveSpecies\", verbose = FALSE)) clonal_diversity_all <- data.frame(Sample = names(genotyping_mt_all), EffectiveSpecies = clonal_diversity_all) knitr::kable(clonal_diversity_all, format=\"html\")"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"cell-mixture-analysis-using-sigurd","dir":"Articles","previous_headings":"","what":"Cell Mixture Analysis using SIGURD","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"data set, chronic myelogenous leukemia cells (K562) brain tumor cells (BT142) mixed sequenced using Seq-Well S3. cells can separated using expression marker genes. original script identifies 6 variants can distinguish two cell types. reproduction, show analysis can faithfully reproduced using streamlined set functions. greatly simplifies analysis. Using set dedicated functions, analysis can now also easily adopted new data sets.","code":""},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"loading-necessary-packages-","dir":"Articles","previous_headings":"","what":"Loading necessary packages.","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"load data MAESTER.","code":"print(\"Libraries for SIGURD.\") ## [1] \"Libraries for SIGURD.\" suppressPackageStartupMessages(library(sigurd)) suppressPackageStartupMessages(library(SummarizedExperiment)) suppressPackageStartupMessages(library(ggplot2))"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"we-load-the-seurat-object-for-the-scrna-seq-data-","dir":"Articles","previous_headings":"","what":"We load the Seurat object for the scRNA-seq data.","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"","code":"seu <- readRDS(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/SW_CellLineMix_Seurat_Keep_Renamed.rds\")"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"loading-the-data-using-sigurd-","dir":"Articles","previous_headings":"","what":"Loading the data using SIGURD.","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"SIGURD loads data automatically reformats data. code uses dedicated functions load process data, streamlines analysis quite substantially.","code":"# The design matrix contains information for the genotyping data. genotyping <- LoadingMAEGATK_typewise(patient = \"SW\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv\", min_cells = 0, type_use = \"Amplicon_MT\", verbose = FALSE)  # Removing cells that are not in the Seurat object. genotyping <- Filtering(genotyping, cells_include = colnames(seu)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" # Adding meta data do the SIGURD object. colData(genotyping)$CellType <- seu$CellType"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"selecting-the-variants-of-interest","dir":"Articles","previous_headings":"","what":"Selecting the Variants of Interest","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"Now, select variants interest.","code":"# Selecting informative variants.  voi.ch.sigurd <- VariantSelection_Quantile(genotyping, min_coverage = 20, min_quality = 30, quantiles = c(0.1, 0.9), thresholds = c(0.1, 0.9), verbose = FALSE) print(voi.ch.sigurd) ## [1] \"chrM_709_G_A\"  \"chrM_1888_G_A\" \"chrM_1420_T_C\" \"chrM_2141_T_C\" ## [5] \"chrM_9117_T_C\" \"chrM_7990_C_T\""},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"visualisation-using-sigurd","dir":"Articles","previous_headings":"","what":"Visualisation using SIGURD","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"","code":"# Determining if a cell is supporting one of the two cell types. cell_support <- CallSupport(SE = genotyping, VOI_group1 = voi.ch.sigurd[voi.ch.sigurd != \"chrM_7990_C_T\"], VOI_group2 = \"chrM_7990_C_T\", group1_name = \"K562\", group2_name = \"BT142\", min_mutated_reads = 3, min_reads = 30, group_factor = 10, verbose = FALSE, return_nonsupport = TRUE) colData(genotyping)$CellType_MT <- cell_support$Support cell_support <- subset(cell_support, Support %in% c(\"K562\", \"BT142\")) # Selecting only cells with sufficient support for a set of variants.  # Plotting the results on a heatmap. HeatmapVoi(SE = genotyping[,cell_support$Cell], voi = voi.ch.sigurd, annotation_trait = \"CellType\", minimum_coverage = 3, remove_empty_cells = FALSE)"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"selecting-variants-with-comparatively-high-vaf-between-groups","dir":"Articles","previous_headings":"","what":"Selecting variants with comparatively high VAF between groups","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"now select variants higher VAF K562 cells BT142 cells.","code":"voi.ch.lineages <- sigurd::VariantSelection_Group(SE = genotyping, min_coverage = 20, quantiles = c(0.01, 0.99), thresholds = c(0.01, 0.02), min_quality = 30,                                                   group_of_interest = \"CellType_MT\", group1 = \"K562\", group2 = \"BT142\", group_factor = 5, remove_nocall = FALSE, verbose = FALSE) voi.ch.lineages <- gsub(\"chrM_9117_T_C\", \"chrM_2141_T_C\", voi.ch.lineages) # Replace chrM_9117_T_C, which comes up because it has no coverage in some cells, with another homoplasmic variant (chrM_2141_T_C), that has better coverage) voi.ch.lineages <- voi.ch.lineages[!voi.ch.lineages %in% c(\"chrM_5378_A_G\", \"chrM_6384_G_A\")] # These variants are not detected in the bulk data and were removed by hand. print(voi.ch.lineages) ##  [1] \"chrM_1197_G_A\" \"chrM_1227_G_A\" \"chrM_1327_G_A\" \"chrM_1982_G_A\" ##  [5] \"chrM_2008_G_A\" \"chrM_2147_G_A\" \"chrM_2170_G_A\" \"chrM_2478_G_A\" ##  [9] \"chrM_2571_G_A\" \"chrM_2573_G_A\" \"chrM_2810_G_A\" \"chrM_2943_G_A\" ## [13] \"chrM_5274_G_A\" \"chrM_8155_G_A\" \"chrM_8213_G_A\" \"chrM_8278_C_A\" ## [17] \"chrM_9778_G_A\" \"chrM_2141_T_C\" \"chrM_1310_C_T\" \"chrM_1352_C_T\" ## [21] \"chrM_1533_C_T\" \"chrM_9757_C_T\""},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"visualisation-using-sigurd-1","dir":"Articles","previous_headings":"","what":"Visualisation using SIGURD","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"","code":"# Plotting the results on a heatmap. cell_support <- subset(cell_support, Support == \"K562\") genotyping <- Filtering(genotyping, cells_include = cell_support$Cell, verbose = FALSE) HeatmapVoi(SE = genotyping, voi = voi.ch.lineages, minimum_coverage = 3, sort_cells = TRUE, cluster_variants = TRUE)"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"cell-mixture-experiment-using-10x-genomics-sequencing","dir":"Articles","previous_headings":"","what":"Cell Mixture Experiment using 10X Genomics Sequencing","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":", reproduce analysis cell mixture experiment.","code":""},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"loading-necessary-packages-","dir":"Articles","previous_headings":"","what":"Loading necessary packages.","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"load data MAESTER.","code":"print(\"Libraries for SIGURD.\") ## [1] \"Libraries for SIGURD.\" suppressPackageStartupMessages(library(sigurd)) suppressPackageStartupMessages(library(SummarizedExperiment)) suppressPackageStartupMessages(library(ggplot2))"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"we-load-the-seurat-object-for-the-scrna-seq-data-","dir":"Articles","previous_headings":"","what":"We load the Seurat object for the scRNA-seq data.","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"","code":"seu <- readRDS(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/TenX_CellLineMix_Seurat_Keep_Renamed.rds\")"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"loading-the-data-using-sigurd-","dir":"Articles","previous_headings":"","what":"Loading the data using SIGURD.","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"","code":"# The design matrix contains information for the genotyping data. genotyping <- LoadingMAEGATK_typewise(patient = \"TenX\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv\", min_cells = 0, type_use = \"Amplicon_MT\", verbose = FALSE)  # Removing cells that are not in the Seurat object. genotyping <- Filtering(genotyping, cells_include = colnames(seu)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" # Adding meta data do the SIGURD object. colData(genotyping)$CellType <- seu$CellType"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"selecting-the-variants-of-interest","dir":"Articles","previous_headings":"","what":"Selecting the Variants of Interest","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"","code":"# Selecting informative variants.  voi.ch.sigurd <- VariantSelection_Quantile(genotyping, min_coverage = 20, min_quality = 30, quantiles = c(0.1, 0.9), thresholds = c(0.1, 0.9), verbose = FALSE) print(voi.ch.sigurd) ##  [1] \"chrM_709_G_A\"   \"chrM_1888_G_A\"  \"chrM_6249_G_A\"  \"chrM_8697_G_A\"  ##  [5] \"chrM_11719_G_A\" \"chrM_15452_C_A\" \"chrM_1420_T_C\"  \"chrM_2141_T_C\"  ##  [9] \"chrM_4216_T_C\"  \"chrM_6524_T_C\"  \"chrM_9117_T_C\"  \"chrM_11251_A_G\" ## [13] \"chrM_11764_A_G\" \"chrM_11812_A_G\" \"chrM_15607_A_G\" \"chrM_7990_C_T\"  ## [17] \"chrM_12741_C_T\""},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"visualisation-using-sigurd","dir":"Articles","previous_headings":"","what":"Visualisation using SIGURD","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"","code":"# Determining if a cell is supporting one of the two cell types. cell_support <- CallSupport(SE = genotyping, VOI_group1 = voi.ch.sigurd[voi.ch.sigurd != \"chrM_7990_C_T\"], VOI_group2 = \"chrM_7990_C_T\", group1_name = \"K562\", group2_name = \"BT142\", min_mutated_reads = 3, min_reads = 30, group_factor = c(10,2), verbose = FALSE) genotyping <- Filtering(genotyping, cells_include = cell_support$Cell) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" colData(genotyping)$CellType_MT <- cell_support$Support cell_support <- subset(cell_support, Support %in% c(\"K562\", \"BT142\")) # Selecting only cells with sufficient support for a set of variants.  # Plotting the results on a heatmap. HeatmapVoi(SE = genotyping, voi = voi.ch.sigurd, annotation_trait = \"CellType\", minimum_coverage = 3)"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"selecting-variants-with-comparatively-high-vaf-between-groups","dir":"Articles","previous_headings":"","what":"Selecting variants with comparatively high VAF between groups","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"now select variants higher VAF K562 cells BT142 cells.","code":"voi.ch.lineages <- sigurd::VariantSelection_Group(SE = genotyping, min_coverage = 100, quantiles = c(0.01, 0.99), thresholds = c(0.01, 0.02), min_quality = 30,                                                   group_of_interest = \"CellType_MT\", group1 = \"K562\", group2 = \"BT142\", group_factor = 5, remove_nocall = FALSE, verbose = FALSE) voi.ch.lineages <- voi.ch.lineages[!voi.ch.lineages %in% c(\"chrM_8251_G_A\", \"chrM_7693_C_T\")] # These variants are not detected in the bulk data and were removed by hand. voi.ch.lineages <- c(voi.ch.lineages, \"chrM_2141_T_C\") # Adding a homoplasmic variant as positive control. print(voi.ch.lineages) ##  [1] \"chrM_1916_G_A\"  \"chrM_2008_G_A\"  \"chrM_2147_G_A\"  \"chrM_2551_G_A\"  ##  [5] \"chrM_2571_G_A\"  \"chrM_2573_G_A\"  \"chrM_7269_G_A\"  \"chrM_7337_G_A\"  ##  [9] \"chrM_7362_G_A\"  \"chrM_7706_G_A\"  \"chrM_8155_G_A\"  \"chrM_9247_G_A\"  ## [13] \"chrM_9778_G_A\"  \"chrM_10223_C_A\" \"chrM_11531_G_A\" \"chrM_11914_G_A\" ## [17] \"chrM_15374_G_A\" \"chrM_8211_T_C\"  \"chrM_9613_T_C\"  \"chrM_1733_C_T\"  ## [21] \"chrM_2357_C_T\"  \"chrM_2574_G_T\"  \"chrM_7825_C_T\"  \"chrM_9757_C_T\"  ## [25] \"chrM_9822_C_T\"  \"chrM_11965_C_T\" \"chrM_12102_C_T\" \"chrM_2141_T_C\" # Plotting the results on a heatmap. cell_support <- subset(cell_support, Support == \"K562\") # Only plotting K562 cells. genotyping <- Filtering(genotyping, cells_include = cell_support$Cell, verbose = FALSE) HeatmapVoi(SE = genotyping, voi = voi.ch.lineages, minimum_coverage = 3, sort_cells = TRUE, cluster_variants = TRUE)"},{"path":"https://costalab.github.io/sigurd/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Martin Grasshoff. Author, maintainer. Ivan Costa. Author.","code":""},{"path":"https://costalab.github.io/sigurd/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Grasshoff M, Costa (2024). sigurd: Single cell Genotyping Using RNA Data. R package version 0.3.1, https://costalab.github.io/sigurd/.","code":"@Manual{,   title = {sigurd: Single cell Genotyping Using RNA Data},   author = {Martin Grasshoff and Ivan Costa},   year = {2024},   note = {R package version 0.3.1},   url = {https://costalab.github.io/sigurd/}, }"},{"path":"https://costalab.github.io/sigurd/index.html","id":"single-cell-genotyping-using-rna-data-sigurd","dir":"","previous_headings":"","what":"Single cell Genotyping Using RNA Data","title":"Single cell Genotyping Using RNA Data","text":"Martin Graßhoff1 Ivan G. Costa1 1Institute Computational Genomics, Faculty Medicine, RWTH Aachen University, Aachen, 52074 Germany Motivation: advent single RNA seq assays, became possible determine mutational status individual cell. Single cell RNA seq data nature sparse probability hitting specific variants interest therefore low. issue can overcome using modified amplicon assays, also possible impute mutational status using correlation detected mitochondrial somatic variants. Results: Sigurd R package analysis single cell data. determine overall variant burden per cell also number interesting mitochondrial variants using previously published approaches. employ imputation approach utilizes correlation mitochondrial variants somatic variants. Mitochondrial mutations significantly associated somatic mutations used stand-ins.","code":""},{"path":"https://costalab.github.io/sigurd/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Single cell Genotyping Using RNA Data","text":"can install sigurd using following code. vignette requires data currently published, provided reference.","code":"install.packages(\"devtools\") devtools::install_github(\"https://github.com/CostaLab/sigurd.git\", build_vignettes = FALSE) require(sigurd)"},{"path":"https://costalab.github.io/sigurd/index.html","id":"sigurd","dir":"","previous_headings":"","what":"SIGURD","title":"Single cell Genotyping Using RNA Data","text":"provided small example data set SiGURD. consists chromosome 9 MT one MPN sample. mutation data obtained Sanger Institute Catalogue Somatic Mutations Cancer web site, http://cancer.sanger.ac.uk/cosmic Bamford et al (2004) COSMIC (Catalogue Somatic Mutations Cancer) database website. Br J Cancer, 91,355-358.","code":"# This will be included for published data. # vignette('sigurd')"},{"path":"https://costalab.github.io/sigurd/index.html","id":"current-features-v0-3-1","dir":"","previous_headings":"","what":"Current Features v0.3.1","title":"Single cell Genotyping Using RNA Data","text":"Loading data VarTrix MAEGATK. Transforming data compatible joint analysis. Calculating variant burden per cell. Thresholding variants using approach described Miller et al. [2] Finding associated variants using correlation Fisher Test.","code":""},{"path":"https://costalab.github.io/sigurd/index.html","id":"sources","dir":"","previous_headings":"","what":"Sources","title":"Single cell Genotyping Using RNA Data","text":"package implements approaches following packages respositories: - https://github.com/petervangalen/MAESTER-2021 – Variant Thresholding functions loading MAEGATK data. - https://github.com/CostaLab/CimpleG – loading saving function.","code":""},{"path":"https://costalab.github.io/sigurd/index.html","id":"future","dir":"","previous_headings":"","what":"Future","title":"Single cell Genotyping Using RNA Data","text":"Memory optimization Loading CB sniffer results Providing data vignette","code":""},{"path":"https://costalab.github.io/sigurd/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"Single cell Genotyping Using RNA Data","text":"[1] VarTrix. github [2] Miller, T.E., et al. Mitochondrial variant enrichment high-throughput single-cell RNA sequencing resolves clonal populations. Nat Biotechnol (2022). link. See also: MAEGATK Analysis, Data","code":""},{"path":"https://costalab.github.io/sigurd/reference/AllelFrequencyFoldChange.html","id":null,"dir":"Reference","previous_headings":"","what":"AllelFrequencyFoldChange — AllelFrequencyFoldChange","title":"AllelFrequencyFoldChange — AllelFrequencyFoldChange","text":"Check cell supported set variants.","code":""},{"path":"https://costalab.github.io/sigurd/reference/AllelFrequencyFoldChange.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"AllelFrequencyFoldChange — AllelFrequencyFoldChange","text":"","code":"AllelFrequencyFoldChange(   SE,   VOI = NULL,   group_of_interest,   group1 = \"group1\",   group2 = \"group2\",   maximum_foldchange = NULL,   minimum_foldchange = NULL,   minimum_coverage = NULL,   minimum_allele_freq = NULL,   maximum_allele_freq = NULL,   verbose = FALSE )"},{"path":"https://costalab.github.io/sigurd/reference/AllelFrequencyFoldChange.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"AllelFrequencyFoldChange — AllelFrequencyFoldChange","text":"SE SummarizedExperiment object. VOI variants variants analyzed. NULL used. group_of_interest column data divides cells. group1 first group. group2 second group. maximum_foldchange Maximum fold change. minimum_foldchange Minimum fold change. minimum_coverage Minimum coverage variant. minimum_allele_freq Minimum allele frequency groups. maximum_allele_freq Maximum allele frequency groups. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing.html","id":null,"dir":"Reference","previous_headings":"","what":"Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing","title":"Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing","text":"replace values scRNAseq experiment values amplicon experiment.","code":""},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing","text":"","code":"AmpliconSupplementing(scRNAseq, amplicon, verbose = TRUE)"},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing","text":"scRNAseq SummarizedExperiment object containing scRNAseq data. amplicon SummarizedExperiment object containing amplicon data. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing_big.html","id":null,"dir":"Reference","previous_headings":"","what":"Supplementing scRNAseq values with Amplicon values using big.matrix — AmpliconSupplementing_big","title":"Supplementing scRNAseq values with Amplicon values using big.matrix — AmpliconSupplementing_big","text":"replace values scRNAseq experiment values amplicon experiment.","code":""},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supplementing scRNAseq values with Amplicon values using big.matrix — AmpliconSupplementing_big","text":"","code":"AmpliconSupplementing_big(scRNAseq, amplicon)"},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Supplementing scRNAseq values with Amplicon values using big.matrix — AmpliconSupplementing_big","text":"scRNAseq SummarizedExperiment object containing scRNAseq data. amplicon SummarizedExperiment object containing amplicon data.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateAlleleFrequency.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculating the Minor Allele Frequency. — CalculateAlleleFrequency","title":"Calculating the Minor Allele Frequency. — CalculateAlleleFrequency","text":"calculate MAF reference reads matrix alternative reads matrix. function intended used mitochondrial genome somatic mutations.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateAlleleFrequency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculating the Minor Allele Frequency. — CalculateAlleleFrequency","text":"","code":"CalculateAlleleFrequency(reference_reads, alternative_reads, pseudo_count = 0)"},{"path":"https://costalab.github.io/sigurd/reference/CalculateAlleleFrequency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculating the Minor Allele Frequency. — CalculateAlleleFrequency","text":"reference_reads Reference reads matrix. alternative_reads List matrices alternative reads. pseudo_count = pseudo count want add reference_reads matrix. Default = 0","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateAltReads.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateAltReads — CalculateAltReads","title":"CalculateAltReads — CalculateAltReads","text":"calculate number reads covering variant using forward reverse reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateAltReads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateAltReads — CalculateAltReads","text":"","code":"CalculateAltReads(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateAltReads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateAltReads — CalculateAltReads","text":"SE SummarizedExperiment object. chromosome_prefix List matrices alternative reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateConsensus.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateConsensus — CalculateConsensus","title":"CalculateConsensus — CalculateConsensus","text":"calculate consensus information MAEGATK results. set cells alternative reads 2 (Alternative). set cells reference reads 1 (Reference). set cells mixture alternative reference reads 3 (). set cells reads 0 (NoCall). Please note. Cells can reads reference specific variant reads alternative. cell can still reads alternative alleles. cell still considered 0 (NoCall) variant. example: cell position 3: 0 reads, 53 T reads, 63 C reads, 148 T reads. variant chrM_3_T_A, cell 53 reference reads, also reads variants position. make sure confusion, cell set NoCall.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateConsensus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateConsensus — CalculateConsensus","text":"","code":"CalculateConsensus(SE, chromosome_prefix = \"chrM\", verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/reference/CalculateConsensus.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateConsensus — CalculateConsensus","text":"SE SummarizedExperiment object. chromosome_prefix chromosome name used prefix. verbose function verbose? Default = FALSE","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateCorrelationPValue.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlating the SNVs — CalculateCorrelationPValue","title":"Correlating the SNVs — CalculateCorrelationPValue","text":"perform correlation SNVs calculate P values.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateCorrelationPValue.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlating the SNVs — CalculateCorrelationPValue","text":"","code":"CalculateCorrelationPValue(   variant_values,   other_mutation,   all_variants_list,   min_intersecting_cells = 5 )"},{"path":"https://costalab.github.io/sigurd/reference/CalculateCorrelationPValue.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlating the SNVs — CalculateCorrelationPValue","text":"variant_values fraction values analysing. vector. other_mutation variants . vector variant names. all_variants_list List fraction values variants want compare variant . min_intersecting_cells Minimum number intersecting cells. Correlations less performed.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateCoverage — CalculateCoverage","title":"CalculateCoverage — CalculateCoverage","text":"calculate coverage information per variant MAEGATK results.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateCoverage — CalculateCoverage","text":"","code":"CalculateCoverage(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateCoverage — CalculateCoverage","text":"SE SummarizedExperiment object. chromosome_prefix List matrices alternative reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateFisherTestPValue — CalculateFisherTestPValue","title":"CalculateFisherTestPValue — CalculateFisherTestPValue","text":"perform Fisher Test SNVs calculate P values.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateFisherTestPValue — CalculateFisherTestPValue","text":"","code":"CalculateFisherTestPValue(   variant_values,   other_mutation,   all_variants_list,   min_intersecting_cells = 5 )"},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateFisherTestPValue — CalculateFisherTestPValue","text":"variant_values fraction values analysing. vector. other_mutation variants . vector variant names. all_variants_list List fraction values variants want compare variant . min_intersecting_cells Minimum number intersecting cells. Correlations less performed.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue2.html","id":null,"dir":"Reference","previous_headings":"","what":"We perform the Fisher test of SNVs and calculate the P values. — CalculateFisherTestPValue2","title":"We perform the Fisher test of SNVs and calculate the P values. — CalculateFisherTestPValue2","text":"perform Fisher test SNVs calculate P values.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"We perform the Fisher test of SNVs and calculate the P values. — CalculateFisherTestPValue2","text":"","code":"CalculateFisherTestPValue2(   variant_values,   other_mutation,   all_variants_list,   min_intersecting_cells = 5 )"},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"We perform the Fisher test of SNVs and calculate the P values. — CalculateFisherTestPValue2","text":"variant_values fraction values analysing. vector. other_mutation variants . vector variant names. all_variants_list List fraction values variants want compare variant . min_intersecting_cells Minimum number intersecting cells. Correlations less performed.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateQuality.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateQuality — CalculateQuality","title":"CalculateQuality — CalculateQuality","text":"calculate quality per variant.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateQuality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateQuality — CalculateQuality","text":"","code":"CalculateQuality(SE, variants, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateQuality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateQuality — CalculateQuality","text":"SE SummarizedExperiment object. variants variants want get quality . chromosome_prefix List matrices alternative reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateRefReads.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateRefReads — CalculateRefReads","title":"CalculateRefReads — CalculateRefReads","text":"calculate number reference reads covering variant using forward reverse reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateRefReads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateRefReads — CalculateRefReads","text":"","code":"CalculateRefReads(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateRefReads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateRefReads — CalculateRefReads","text":"SE SummarizedExperiment object. chromosome_prefix List matrices reference reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateStrandCorrelation.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateStrandCorrelation — CalculateStrandCorrelation","title":"CalculateStrandCorrelation — CalculateStrandCorrelation","text":"calculate correlation amount forward reverse reads per variant.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateStrandCorrelation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateStrandCorrelation — CalculateStrandCorrelation","text":"","code":"CalculateStrandCorrelation(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateStrandCorrelation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateStrandCorrelation — CalculateStrandCorrelation","text":"SE SummarizedExperiment object. chromosome_prefix List matrices alternative reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CallSupport.html","id":null,"dir":"Reference","previous_headings":"","what":"CallSupport — CallSupport","title":"CallSupport — CallSupport","text":"Check cell supported set variants.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CallSupport.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CallSupport — CallSupport","text":"","code":"CallSupport(   SE,   VOI_group1,   VOI_group2,   group1_name = \"group1\",   group2_name = \"group2\",   min_mutated_reads = 3,   min_reads = 30,   group_factor = NULL,   verbose = TRUE,   return_nonsupport = FALSE )"},{"path":"https://costalab.github.io/sigurd/reference/CallSupport.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CallSupport — CallSupport","text":"SE SummarizedExperiment object. VOI_group1 variants supporting first group. VOI_group2 variants supporting second group. group1_name name used first group. group2_name name used second group. min_mutated_reads minimum number mutated reads cell supporting group. min_reads Minimum number reads per cell classification. group_factor much higher mean allele frequency group 1 compared group 2 vice versa? Can vector length 2. verbose function verbose? Default = TRUE return_nonsupport nonsupporting cells return ? Default FALSE. group_of_interest column data divides cells.","code":""},{"path":"https://costalab.github.io/sigurd/reference/ClonalDefinition.html","id":null,"dir":"Reference","previous_headings":"","what":"Defining clones. — ClonalDefinition","title":"Defining clones. — ClonalDefinition","text":"function defines clones using combination variants supplied. set variants can paired identity, like sample cell type. clones determined respect group. information provided, clones determined cells present.","code":""},{"path":"https://costalab.github.io/sigurd/reference/ClonalDefinition.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Defining clones. — ClonalDefinition","text":"","code":"ClonalDefinition(   se,   variants_ls,   grouping = NULL,   identities = NULL,   explicit = FALSE,   explicit_not = NULL,   explicit_min_vaf = 0.01,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/ClonalDefinition.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Defining clones. — ClonalDefinition","text":"se SummarizedExperiment object. variants_ls List variants clonal definition grouping meta data    column used split cells groups. Default = NULL identities Vector groups, like samples. explicit want specify variants forming clone? variant_ls needs list variants define clone. One variant per group. explicit_not want specify set variants cell may ? One set per group. explicit_min_vaf Minimum VAF cell considered positive. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/ClonalDiversity.html","id":null,"dir":"Reference","previous_headings":"","what":"Determining the clonal diversity. — ClonalDiversity","title":"Determining the clonal diversity. — ClonalDiversity","text":"function determines clonal diversity. clones defined using function ClonalDefinition. required use clones, column column data object can used.","code":""},{"path":"https://costalab.github.io/sigurd/reference/ClonalDiversity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determining the clonal diversity. — ClonalDiversity","text":"","code":"ClonalDiversity(   se,   grouping = \"Clones\",   cells = NULL,   diversity_measure = \"EffectiveSpecies\",   base = exp(1),   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/ClonalDiversity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determining the clonal diversity. — ClonalDiversity","text":"se SummarizedExperiment object. grouping meta data    column used. cells cells used? NULL uses cells. diversity_measure diversity measure calculated? Can EffectiveSpecies, shannon, simpson, invsimpson base base diversity verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects.html","id":null,"dir":"Reference","previous_headings":"","what":"CombineSEobjects — CombineSEobjects","title":"CombineSEobjects — CombineSEobjects","text":"combine two SummarizedExperiment objects. originally intended add mitochondrial genotyping information somatic genotyping information. function can combine two objects requried two different genotyping results.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CombineSEobjects — CombineSEobjects","text":"","code":"CombineSEobjects(se_1, se_2, suffixes = c(\"_1\", \"_2\"))"},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CombineSEobjects — CombineSEobjects","text":"se_1 SummarizedExperiment object 1. se_2 SummarizedExperiment object 2. suffixes suffixes want add meta data.frame.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects_big.html","id":null,"dir":"Reference","previous_headings":"","what":"CombineSEobjects_big — CombineSEobjects_big","title":"CombineSEobjects_big — CombineSEobjects_big","text":"combine two SummarizedExperiment objects big matrices.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CombineSEobjects_big — CombineSEobjects_big","text":"","code":"CombineSEobjects_big(se_somatic, se_MT, suffixes = c(\"_somatic\", \"_MT\"))"},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CombineSEobjects_big — CombineSEobjects_big","text":"se_somatic SummarizedExperiment object somatic variants. se_MT SummarizedExperiment object MT variants. suffixes suffixes want add meta data.frame.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Enrichment_FisherTest.html","id":null,"dir":"Reference","previous_headings":"","what":"Enrichment_FisherTest — Enrichment_FisherTest","title":"Enrichment_FisherTest — Enrichment_FisherTest","text":"function performs Fisher test. specified variant ","code":""},{"path":"https://costalab.github.io/sigurd/reference/Enrichment_FisherTest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Enrichment_FisherTest — Enrichment_FisherTest","text":"","code":"Enrichment_FisherTest(   se = NULL,   variant = NULL,   use_nocall = FALSE,   both_as_alt = TRUE,   trait = NULL,   trait_levels = NULL )"},{"path":"https://costalab.github.io/sigurd/reference/Enrichment_FisherTest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Enrichment_FisherTest — Enrichment_FisherTest","text":"se SummarizedExperiment object. variant variant analysed. values variant retrieved consensus assay. use_nocall NoCall values used? non genotyped cells separate group addition Alt Ref. FALSE, NoCalls removed. Default = FALSE both_as_alt consensus value heterozyguous (3 ) treated homozyguous (Alt)? Default = TRUE trait trait variant associated . can column colData object. trait_levels trait levels used comparison? example, Sample 1-3 present 1 2 used comparison use trait_levels = c(\"Sample_1\", \"Sample_2\"). NULL uses levels. Default = NULL","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":null,"dir":"Reference","previous_headings":"","what":"Filtering the loaded genotyping data. — Filtering","title":"Filtering the loaded genotyping data. — Filtering","text":"filter SummarizedExperiment object exclude variants cells.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filtering the loaded genotyping data. — Filtering","text":"","code":"Filtering(   SE,   cells_include = NULL,   cells_exclude = NULL,   fraction_threshold = NULL,   alts_threshold = NULL,   min_cells_per_variant = NULL,   min_variants_per_cell = NULL,   reject_value = \"NoCall\",   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filtering the loaded genotyping data. — Filtering","text":"SE SummarizedExperiment object. cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. fraction_threshold Variants VAF threshold set 0. Numeric. Default = NULL. alts_threshold Variants number alt reads less threshold set 0. Numeric. Default = NULL. min_cells_per_variant many cells variant present included? Numeric. Default = 2. min_variants_per_cell many variants covered cell included? Default = 1. reject_value cells fall threshold (fraction_threshold alts_threshold) treated Reference NoCall? Default = NoCall. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Filtering the loaded genotyping data. — Filtering","text":"one sample time. want remove: cells allow list, cells exclusion list, cells least one variant >1 (Reference), variants alternative transcripts, variants always NoCall, set variants VAF threshold NoCall Reference.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Filtering the loaded genotyping data. — Filtering","text":"","code":"if (FALSE) { # \\dontrun{   # Removing all variants that are not detected in at least 2 cells.   # Before we remove the variants, we set fraction value of variants below 0.05 to 0.   se_geno <- Filtering(se_geno, min_cells_per_variant = 2, fraction_threshold = 0.05) } # }"},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":null,"dir":"Reference","previous_headings":"","what":"Filtering the loaded genotyping data using big matrices. — Filtering_big","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"filter SummarizedExperiment object exclude variants cells.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"","code":"Filtering_big(   se,   blacklisted_barcodes_path = NULL,   fraction_threshold = NULL,   path_seurat = NULL,   min_cells_per_variant = 2 )"},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"se SummarizedExperiment object. blacklisted_barcodes_path Barcodes want remove. Path file one column without header. fraction_threshold Variants VAF threshold set 0. Numeric. path_seurat Path Seurat object. Cells present object removed. min_cells_per_variant many cells variant present included? Numeric. Default = 2. min_variants_per_cell many variants covered cell included? Default = 1.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"one sample time. want remove: cells blacklisted, cells Seurat object, cells least one variant >1 (Reference), variants alternative transcripts, variants always NoCall, set variants VAF threshold reference.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"","code":"if (FALSE) {   # Removing all variants that are not detected in at least 2 cells.   # Before we remove the variants, we set fraction value of variants below 0.05 to 0.   se_geno <- Filtering(se_geno, min_cells_per_variant = 2, fraction_threshold = 0.05) }"},{"path":"https://costalab.github.io/sigurd/reference/GetCellInfoPerVariant.html","id":null,"dir":"Reference","previous_headings":"","what":"We get the variant information per cell. — GetCellInfoPerVariant","title":"We get the variant information per cell. — GetCellInfoPerVariant","text":"get variant information per cell.","code":""},{"path":"https://costalab.github.io/sigurd/reference/GetCellInfoPerVariant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"We get the variant information per cell. — GetCellInfoPerVariant","text":"","code":"GetCellInfoPerVariant(se, voi_ch, verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/reference/GetCellInfoPerVariant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"We get the variant information per cell. — GetCellInfoPerVariant","text":"se SummarizedExperiment object. voi_ch Variants interest. verbose function verbose? Default = FALSE","code":""},{"path":"https://costalab.github.io/sigurd/reference/GetVariantInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"GetVariantInfo — GetVariantInfo","title":"GetVariantInfo — GetVariantInfo","text":"get genotyping information set variants. function returns matrix values specified assay.","code":""},{"path":"https://costalab.github.io/sigurd/reference/GetVariantInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GetVariantInfo — GetVariantInfo","text":"","code":"GetVariantInfo(SE, information = \"consensus\", variants = NULL, cells = NULL)"},{"path":"https://costalab.github.io/sigurd/reference/GetVariantInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GetVariantInfo — GetVariantInfo","text":"SE SummarizedExperiment object. information assay desired information. Default: consensus variants vector variants. cells vector cell IDs. default cells returned. Default: NULL","code":""},{"path":"https://costalab.github.io/sigurd/reference/HeatmapVoi.html","id":null,"dir":"Reference","previous_headings":"","what":"HeatmapVoi — HeatmapVoi","title":"HeatmapVoi — HeatmapVoi","text":"plot heatmap set Variants Interest using Variant Allele Frequency values SummarizedExperiment object.","code":""},{"path":"https://costalab.github.io/sigurd/reference/HeatmapVoi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HeatmapVoi — HeatmapVoi","text":"","code":"HeatmapVoi(   SE,   voi,   annotation_trait = NULL,   column_title = NULL,   minimum_coverage = 0,   sort_cells = FALSE,   remove_empty_cells = FALSE,   minimum_allele_freq = 0,   cluster_variants = FALSE,   cluster_variants_distance = \"euclidean\",   cluster_variants_method = \"complete\" )"},{"path":"https://costalab.github.io/sigurd/reference/HeatmapVoi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"HeatmapVoi — HeatmapVoi","text":"SE SummarizedExperiment object. voi Variants Interest. annotation_trait Cell Annotation bottom heat map. column_title title heat map. Default = NULL minimum_coverage minimum coverage per cell plotted. sort_cells cells sorted ordering cells according largest clones? FALSE uses default complete clustering euclidean distance. remove_empty_cells cells fraction 0 variants removed? Default = FALSE minimum_allele_freq Minimum allele frequency include cell. cluster_variants variants clustered? Default FALSE. cluster_variants_distance distance clustering variants. Default euclidean. cluster_variants_method distance variant clustering. Default complete","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingMAEGATK_typewise.html","id":null,"dir":"Reference","previous_headings":"","what":"LoadingMAEGATK_typewise — LoadingMAEGATK_typewise","title":"LoadingMAEGATK_typewise — LoadingMAEGATK_typewise","text":"load MAEGATK output transform compatible VarTrix output. input file specifically formated csv file necessary information run analysis. Note source column input file needs mgaetk mgatk function. case insensitive. want load single sample without use input file, set following variables. samples_path barcodes_path patient samples_file = NULL","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingMAEGATK_typewise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LoadingMAEGATK_typewise — LoadingMAEGATK_typewise","text":"","code":"LoadingMAEGATK_typewise(   samples_file,   patient,   samples_path = NULL,   patient_column = \"patient\",   type_use = \"scRNAseq_MT\",   chromosome_prefix = \"chrM\",   min_cells = 2,   cells_include = NULL,   cells_exclude = NULL,   barcodes_path = NULL,   cellbarcode_length = 18,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingMAEGATK_typewise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"LoadingMAEGATK_typewise — LoadingMAEGATK_typewise","text":"samples_file Path csv file samples loaded. patient patient want load. samples_path Path input folder. patient_column column contains patient information. Use merge, samples merged. type_use type input. rows specified type loaded. chromosome_prefix prefix want use. Default: \"chrM\" min_cells minimum number cells coverage variant. Variants coverage less amount cells removed. Default = 2 cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. barcodes_path Path barcodes file tsv. Default = NULL cellbarcode_length length cell barcode. length actual barcode plus two suffix (-1). Default = 18 verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingRawMatrix_typewise.html","id":null,"dir":"Reference","previous_headings":"","what":"LoadingRawMatrix_typewise — LoadingRawMatrix_typewise","title":"LoadingRawMatrix_typewise — LoadingRawMatrix_typewise","text":"function load dense matrix genotyping information reformat . matrix column cell barcodes, one reference reads one alternative reads. type design matrix used variant name.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingRawMatrix_typewise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LoadingRawMatrix_typewise — LoadingRawMatrix_typewise","text":"","code":"LoadingRawMatrix_typewise(   samples_file,   patient,   patient_column = \"patient\",   variant_use = NULL,   cells_include = NULL,   cells_exclude = NULL,   matrix_column_separator = \",\",   matrix_header = TRUE,   cellbarcode_index = 1,   ref_index = 2,   alt_index = 3,   cellbarcode_length = 18,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingRawMatrix_typewise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"LoadingRawMatrix_typewise — LoadingRawMatrix_typewise","text":"samples_file Path csv file samples loaded. patient patient want load. patient_column column contains patient information. variant_use variant respective matrices. cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. cellbarcode_length length cell barcode. length actual barcode plus two suffix (-1). Default = 18 verbose function verbose? Default = TRUE samples_path Path input folder. Must include barcodes file.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVCF_typewise.html","id":null,"dir":"Reference","previous_headings":"","what":"LoadingVCF_typewise — LoadingVCF_typewise","title":"LoadingVCF_typewise — LoadingVCF_typewise","text":"load cellwise pileup result VCF file. want load single sample without use input file, set following variables. samples_path patient samples_file = NULL Note source column input file needs vcf function. case insensitive. happened reads N allele aligned. can cause problems since variants typically variants lists. can remove variants setting remove_N_alternative TRUE (default). Set option FALSE, really want retain variants.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVCF_typewise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LoadingVCF_typewise — LoadingVCF_typewise","text":"","code":"LoadingVCF_typewise(   samples_file,   samples_path = NULL,   vcf_path,   patient,   patient_column = \"patient\",   type_use = \"scRNAseq_Somatic\",   min_reads = NULL,   min_cells = 2,   cells_include = NULL,   cells_exclude = NULL,   remove_N_alternative = TRUE,   cellbarcode_length = 18,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVCF_typewise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"LoadingVCF_typewise — LoadingVCF_typewise","text":"samples_file Path csv file samples loaded. samples_path Path input folder. vcf_path Path VCF file variants. patient patient want load. patient_column column contains patient information. Use merge, samples merged. type_use type input. rows specified type loaded. min_reads minimum number reads want. Otherwise treat NoCall. Default = NULL. min_cells minimum number cells variant. Otherwise, remove variant. Default = 2. cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. remove_N_alternative Remove variants N alternative, see Description. Default = TRUE cellbarcode_length length cell barcode. length actual barcode plus two suffix (-1). Default = 18 verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix.html","id":null,"dir":"Reference","previous_headings":"","what":"We load the VarTrix results for one patient and merge all types together. — LoadingVarTrix","title":"We load the VarTrix results for one patient and merge all types together. — LoadingVarTrix","text":"load VarTrix results one patient merge types together.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"We load the VarTrix results for one patient and merge all types together. — LoadingVarTrix","text":"","code":"LoadingVarTrix(samples_path, vcf_path, vcf_path_MT, patient)"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"We load the VarTrix results for one patient and merge all types together. — LoadingVarTrix","text":"samples_path Path csv file samples loaded. vcf_path Path VCF file somatic variants. vcf_path_MT Path VCF file MT variants. patient Patient loaded.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":null,"dir":"Reference","previous_headings":"","what":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"function loads VarTrix results outputs list two SummarizedExperiments objects, one somatic variants accompanying mitochondrial variants.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"","code":"LoadingVarTrix(samples_file, vcf_path, vcf_path_MT, patient)"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"samples_file Path input file. One sample per row. contain following columns:patient: patient sample. patient can multiple samples (treated/untreated). samples merged per patient.sample: ID sample.resource: VarTrix MAEGATK input? Must either VarTrix MAEGATK.type: type data? Must one following: scRNAseq_Somatic, scRNAseq_MT, Amplicon_Somatic, Amplicon_MT.input_folder: Path folder, VarTrix output stored.cells: Path barcodes file CellRanger output. vcf_path Path VCF file contains somatic variants interested . vcf_path_MT Path VCF file contains MT variants interested . patient patient want load.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"function loads VarTrix one patients input file. patient multiple samples, samples merged. two types input data, single cell RNA sequencing amplicon data. scRNAseq data result something like 10X assay, amplicon data focuses specific part genome. output CellRanger pipeline. Amplicon data much higher coverage specific area therefore much better areas. scRNAseq data overwritten amplicon data available. output list two SummarizedExperiment objects. object contains two assays:consensus_somatic: consensus information per somatic variant cell.consensus_MT: consensus information per MT variant cell.fraction_somatic: variant allele frequency per somatic variant cell.fraction_MT: variant allele frequency per MT variant cell. consensus information encoded following way:0: Call, reads covering position.1: Reference, reference reads cover position.2: Alternative, mutated reads cover position.3: , alt ref reads cover position.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"return list two objects. SE_Somatic somatic variants results. SE_MT MT variants results.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise.html","id":null,"dir":"Reference","previous_headings":"","what":"LoadingVarTrix_typewise — LoadingVarTrix_typewise","title":"LoadingVarTrix_typewise — LoadingVarTrix_typewise","text":"load different types results (scRNAseq/amplicon MT/amplicon), might need extreme amounts memory. solve issue, load type separately. following function (AmpliconSupplementing), can add amplicon information scRNAseq information. input file specifically formatted csv file necessary information run analysis. Note source column input file needs vartrix function. hard coded case insensitive.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LoadingVarTrix_typewise — LoadingVarTrix_typewise","text":"","code":"LoadingVarTrix_typewise(   samples_file,   samples_path = NULL,   barcodes_path = NULL,   snp_path = NULL,   vcf_path,   patient,   patient_column = \"patient\",   type_use = \"scRNAseq_Somatic\",   min_reads = NULL,   min_cells = 2,   cells_include = NULL,   cells_exclude = NULL,   cellbarcode_length = 18,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"LoadingVarTrix_typewise — LoadingVarTrix_typewise","text":"samples_file Path csv file samples loaded. samples_path Path input folder. Must include barcodes file. barcodes_path path cell barcodes tsv. Default = NULL snp_path Path SNP file used VarTrix (SNV.loci.txt). vcf_path Path VCF file variants. patient patient want load. patient_column column contains patient information. Use merge, samples merged. type_use type input. rows specified type loaded. min_reads minimum number reads want. Otherwise treat NoCall. Default = NULL. min_cells minimum number cells variant. Otherwise, remove variant. Default = 2. cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. cellbarcode_length length cell barcode. length actual barcode plus two suffix (-1). Default = 18 verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise_big.html","id":null,"dir":"Reference","previous_headings":"","what":"Loading VarTrix results using big.matrix — LoadingVarTrix_typewise_big","title":"Loading VarTrix results using big.matrix — LoadingVarTrix_typewise_big","text":"load different types results (scRNAseq/amplicon MT/amplicon), might need extreme amounts memory. solve issue, load type separately. following function (AmpliconSupplementing), can add amplicon information scRNAseq information.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Loading VarTrix results using big.matrix — LoadingVarTrix_typewise_big","text":"","code":"LoadingVarTrix_typewise_big(   samples_file,   samples_path = NULL,   barcodes_path = NULL,   snp_path = NULL,   vcf_path,   patient,   sample = NULL,   type_use = \"scRNAseq_Somatic\",   min_reads = 3,   min_cells = 2 )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Loading VarTrix results using big.matrix — LoadingVarTrix_typewise_big","text":"samples_file Path csv file samples loaded. samples_path Path input folder. barcodes_path Path barcodes file. vcf_path Path VCF file variants. patient patient want load. type_use type input. one : scRNAseq_Somatic, Amplicon_Somatic, scRNAseq_MT, Amplicon_MT. min_reads minimum number reads want. Otherwise treat NoCall. yet implemented. min_cells minimum number cells variant. Otherwise, remove variant.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Merging_SE_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Merging list of SummarizedExperiment objects. — Merging_SE_list","title":"Merging list of SummarizedExperiment objects. — Merging_SE_list","text":"function wrapper .(\"cbind\", se).","code":""},{"path":"https://costalab.github.io/sigurd/reference/Merging_SE_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merging list of SummarizedExperiment objects. — Merging_SE_list","text":"","code":"Merging_SE_list(se)"},{"path":"https://costalab.github.io/sigurd/reference/Merging_SE_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merging list of SummarizedExperiment objects. — Merging_SE_list","text":"se SummarizedExperiment object","code":""},{"path":"https://costalab.github.io/sigurd/reference/RowWiseSplit.html","id":null,"dir":"Reference","previous_headings":"","what":"RowWiseSplit — RowWiseSplit","title":"RowWiseSplit — RowWiseSplit","text":"Performing correlation Fisher test association SummarizedExperiment object requires extreme amounts memory. reduce amount memory necessary, instead get individual rows consensus assay. can remove NoCalls (reads) individual vectors, reducing amount memory needed.","code":""},{"path":"https://costalab.github.io/sigurd/reference/RowWiseSplit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RowWiseSplit — RowWiseSplit","text":"","code":"RowWiseSplit(se, n_cores = 1, minimum_reads, remove_nocalls = TRUE)"},{"path":"https://costalab.github.io/sigurd/reference/RowWiseSplit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RowWiseSplit — RowWiseSplit","text":"se SummarizedExperiment object. n_cores Number cores use. remove_nocalls want remove NoCall cells?","code":""},{"path":"https://costalab.github.io/sigurd/reference/SeparatingMatrixToList.html","id":null,"dir":"Reference","previous_headings":"","what":"SeparatingMatrixToList — SeparatingMatrixToList","title":"SeparatingMatrixToList — SeparatingMatrixToList","text":"separate matrix variant information list. variant entry list. NoCalls (cells reads covering variant) can removed. function gets called RowWiseSplit return.","code":""},{"path":"https://costalab.github.io/sigurd/reference/SeparatingMatrixToList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SeparatingMatrixToList — SeparatingMatrixToList","text":"","code":"SeparatingMatrixToList(row_use, total_matrix, remove_nocalls = TRUE)"},{"path":"https://costalab.github.io/sigurd/reference/SeparatingMatrixToList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SeparatingMatrixToList — SeparatingMatrixToList","text":"row_use row separate. total_matrix matrix split. remove_nocalls want remove NoCall cells?","code":""},{"path":"https://costalab.github.io/sigurd/reference/SetVariantInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"SetVariantInfo — SetVariantInfo","title":"SetVariantInfo — SetVariantInfo","text":"add genotyping information set variants Seurat object. function returns Seurat object values specified assay added meta data.","code":""},{"path":"https://costalab.github.io/sigurd/reference/SetVariantInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SetVariantInfo — SetVariantInfo","text":"","code":"SetVariantInfo(   SE,   seurat_object,   information = \"consensus\",   variants = NULL,   consensus_character = TRUE,   consensus_group = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/SetVariantInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SetVariantInfo — SetVariantInfo","text":"SE SummarizedExperiment object. seurat_object Seurat object. information assay desired information. Default: consensus variants vector variants. consensus_character consensus information save character value? consensus_group consensus groups Alt merged? effect information consensus.","code":""},{"path":"https://costalab.github.io/sigurd/reference/UMIQC.html","id":null,"dir":"Reference","previous_headings":"","what":"UMIQC — UMIQC","title":"UMIQC — UMIQC","text":"load molecule_info.h5 file CellRanger plot molecules rank. molecule defined combination UMI CB. molecules ranked number replicates.","code":""},{"path":"https://costalab.github.io/sigurd/reference/UMIQC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UMIQC — UMIQC","text":"","code":"UMIQC(   central_input_file = NULL,   molecule_info_path = NULL,   subset_by_cbs = TRUE,   cellbarcodes_path = NULL,   umi_length = 12,   min_reads = 100,   sep = \",\",   samples_column = \"sample\",   molecule_info_column = \"molecule_info\",   cellbarcode_column = \"cells\",   add_10x_suffix = \"-1\" )"},{"path":"https://costalab.github.io/sigurd/reference/UMIQC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UMIQC — UMIQC","text":"central_input_file Path csv file samples loaded. molecule_info_path Path single molecule_info file. subset_by_cbs list cell barcodes molecule_info.h5 file subset list approved cell barcodes? Default: TRUE cellbarcodes_path Path cell barcodes file. used central input file used. umi_length length UMI. Default = 12 min_reads minimum number reads per molecule. sep separator used samples_file. Default: \",\" samples_column column samples samples_file. Default: \"sample\" molecule_info_column column paths molecule_info files samples_file. Default: \"molecule_info\" cellbarcode_column column paths cell barcodes files central input file. Default: \"cells\" add_10x_suffix suffix added cell barcodes? Default 10X standard: \"-1\"","code":""},{"path":"https://costalab.github.io/sigurd/reference/UMI_seq.html","id":null,"dir":"Reference","previous_headings":"","what":"UMI_seq — UMI_seq","title":"UMI_seq — UMI_seq","text":"function converts numeric UMI representation found 10X molecule_info.h5 file character string.","code":""},{"path":"https://costalab.github.io/sigurd/reference/UMI_seq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UMI_seq — UMI_seq","text":"","code":"UMI_seq(number, umi_length = 12)"},{"path":"https://costalab.github.io/sigurd/reference/UMI_seq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UMI_seq — UMI_seq","text":"number numeric expression UMI. umi_length length UMI. Default = 12","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantBurden — VariantBurden","title":"VariantBurden — VariantBurden","text":"Calculate variant burden per cell. simply sum MAF values per cell.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantBurden — VariantBurden","text":"","code":"VariantBurden(se)"},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantBurden — VariantBurden","text":"se SummarizedExperiment object","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden_big.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the variant burden per cell using big matrices. — VariantBurden_big","title":"Calculate the variant burden per cell using big matrices. — VariantBurden_big","text":"Calculate variant burden per cell using big matrices.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the variant burden per cell using big matrices. — VariantBurden_big","text":"","code":"VariantBurden_big(se)"},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the variant burden per cell using big matrices. — VariantBurden_big","text":"se SummarizedExperiment object","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantCloneSizeThresholding.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantCloneSizeThresholding — VariantCloneSizeThresholding","title":"VariantCloneSizeThresholding — VariantCloneSizeThresholding","text":"get variants interest using clone size thresholding. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantCloneSizeThresholding.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantCloneSizeThresholding — VariantCloneSizeThresholding","text":"","code":"VariantCloneSizeThresholding(   SE,   min_coverage = 2,   fraction_negative_cells = 0.9,   min_clone_size = 10,   vaf_threshold = 0.5,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantCloneSizeThresholding.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantCloneSizeThresholding — VariantCloneSizeThresholding","text":"SE SummarizedExperiment object. min_coverage Minimum coverage variant needs . fraction_negative_cells fraction negative cells needed. min_clone_size minimum number cells. vaf_threshold Variant Allele Threshold. Cells threshold considered mutated. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantCorrelationHeatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantCorrelationHeatmap — VariantCorrelationHeatmap","title":"VariantCorrelationHeatmap — VariantCorrelationHeatmap","text":"generate heatmap showing correlation somatic variants MT variants. Packages want remove. see used. ggplot2 parallel rcompanion tidyr","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantCorrelationHeatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantCorrelationHeatmap — VariantCorrelationHeatmap","text":"","code":"VariantCorrelationHeatmap(   correlation_results,   output_path = NULL,   patient,   min_alt_cells = 5,   min_correlation = 0.5,   width_use = 2000,   height_use = 2000,   padding_use = c(165, 165, 2, 2),   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantCorrelationHeatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantCorrelationHeatmap — VariantCorrelationHeatmap","text":"correlation_results Data.frame correlation results. output_path Path output folder. patient patient heatmap. min_alt_cells Minimum number mutated cells needed, otherwise correlation plotted. min_correlation Minimum correlation needed. width_use Width heatmap px. height_use Height heatmap px. padding_use Space around heatmap mm. low, variant names might cut . verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantFisherTestHeatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantFisherTestHeatmap — VariantFisherTestHeatmap","title":"VariantFisherTestHeatmap — VariantFisherTestHeatmap","text":"generate heatmap showing Fisher test somatic variants MT variants. Packages want remove.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantFisherTestHeatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantFisherTestHeatmap — VariantFisherTestHeatmap","text":"","code":"VariantFisherTestHeatmap(   fisher_results,   patient,   min_alt_cells = 5,   min_oddsratio = 1,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantFisherTestHeatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantFisherTestHeatmap — VariantFisherTestHeatmap","text":"fisher_results Data.frame correlation results. patient patient heatmap. min_alt_cells Minimum number mutated cells needed, otherwise association plotted. min_oddsratio Minimum correlation needed. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantQuantileThresholding — VariantQuantileThresholding","title":"VariantQuantileThresholding — VariantQuantileThresholding","text":"get variants interest using quantile thresholding. use top_cells top_VAF, supply one quantil value (quantiles = 0.9, thresholds = 0). function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantQuantileThresholding — VariantQuantileThresholding","text":"","code":"VariantQuantileThresholding(   SE,   min_coverage = 2,   quantiles = c(0.1, 0.9),   thresholds = c(0.1, 0.9),   top_cells = NULL,   top_VAF = NULL,   min_quality = NULL,   mean_allele_frequency = 0,   group_of_interest = NULL,   group1 = NULL,   group2 = NULL,   group_factor = NULL,   remove_nocall = TRUE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantQuantileThresholding — VariantQuantileThresholding","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. top_cells number cells least top_VAF percent variant. top_VAF VAF top cells. min_quality minimum quality want Variants Interest. Can ignored setting NULL. mean_allele_frequency minimum mean allele frequency. Default = 0 group_of_interest column data divides cells. group1 first group interest. set, quantiles calculated group. group2 second group interest. group_factor much higher mean allele frequency group 1 compared group 2? remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding_Combined.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined","title":"VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined","text":"get variants interest using quantile thresholding. function combines functions VariantSelection_Quantile, VariantSelection_Group VariantSelection_TopCells. use top_cells top_VAF, supply one quantil value (quantiles = 0.9, thresholds = 0). function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding_Combined.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined","text":"","code":"VariantQuantileThresholding_Combined(   SE,   min_coverage = 2,   quantiles = c(0.1, 0.9),   thresholds = c(0.1, 0.9),   top_cells = NULL,   top_VAF = NULL,   min_quality = NULL,   mean_allele_frequency = 0,   group_of_interest = NULL,   group1 = NULL,   group2 = NULL,   group_factor = NULL,   remove_nocall = TRUE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding_Combined.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. top_cells number cells least top_VAF percent variant. top_VAF VAF top cells. min_quality minimum quality want Variants Interest. Can ignored setting NULL. mean_allele_frequency minimum mean allele frequency. Default = 0 group_of_interest column data divides cells. group1 first group interest. set, quantiles calculated group. group2 second group interest. group_factor much higher mean allele frequency group 1 compared group 2? remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Group.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantSelection_Group — VariantSelection_Group","title":"VariantSelection_Group — VariantSelection_Group","text":"get variants interest selecting variants high VAF difference two groups. function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Group.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantSelection_Group — VariantSelection_Group","text":"","code":"VariantSelection_Group(   SE,   min_coverage = 2,   quantiles = c(0.1, 0.9),   thresholds = c(0.1, 0.9),   min_quality = NULL,   mean_allele_frequency = 0,   group_of_interest = NULL,   group1 = NULL,   group2 = NULL,   group_factor = 5,   remove_nocall = TRUE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Group.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantSelection_Group — VariantSelection_Group","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. min_quality minimum quality want Variants Interest. Can ignored setting NULL. mean_allele_frequency minimum mean allele frequency. Default = 0 group_of_interest column data divides cells. group1 first group interest. set, quantiles calculated group. group2 second group interest. group_factor much higher mean allele frequency group 1 compared group 2? remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantSelection_Quantile — VariantSelection_Quantile","title":"VariantSelection_Quantile — VariantSelection_Quantile","text":"get variants interest using quantile thresholding. function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantSelection_Quantile — VariantSelection_Quantile","text":"","code":"VariantSelection_Quantile(   SE,   min_coverage = 2,   quantiles = c(0.1, 0.9),   thresholds = c(0.1, 0.9),   min_quality = NULL,   mean_allele_frequency = 0,   remove_nocall = FALSE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantSelection_Quantile — VariantSelection_Quantile","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. min_quality minimum quality want Variants Interest. Can ignored setting NULL. mean_allele_frequency minimum mean allele frequency. Default = 0 remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_TopCells.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantSelection_TopCells — VariantSelection_TopCells","title":"VariantSelection_TopCells — VariantSelection_TopCells","text":"get variants interest selecting small number cells high VAF variant. function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_TopCells.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantSelection_TopCells — VariantSelection_TopCells","text":"","code":"VariantSelection_TopCells(   SE,   min_coverage = 2,   quantiles = 0.9,   thresholds = 0,   top_cells = 10,   top_VAF = 0.5,   min_quality = NULL,   remove_nocall = TRUE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_TopCells.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantSelection_TopCells — VariantSelection_TopCells","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. min_quality minimum quality want Variants Interest. Can ignored setting NULL. remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseCorrelation.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantWiseCorrelation — VariantWiseCorrelation","title":"VariantWiseCorrelation — VariantWiseCorrelation","text":"correlate variants using Pearson correlation. function calls CalculateCorrelationPValue perform actual correlation.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseCorrelation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantWiseCorrelation — VariantWiseCorrelation","text":"","code":"VariantWiseCorrelation(   variants_list,   n_cores = 1,   p_value_adjustment = \"fdr\",   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseCorrelation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantWiseCorrelation — VariantWiseCorrelation","text":"variants_list List fraction values. n_cores Number cores want use. Numeric. p_value_adjustment Method P value adjustment. See p.adjust details. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseFisherTest.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantWiseFisherTest — VariantWiseFisherTest","title":"VariantWiseFisherTest — VariantWiseFisherTest","text":"perform Fisher test determine variants associated. function calls CalculateFisherTestPValue perform actual testing.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseFisherTest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantWiseFisherTest — VariantWiseFisherTest","text":"","code":"VariantWiseFisherTest(   variants_list,   n_cores = 1,   p_value_adjustment = \"fdr\",   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseFisherTest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantWiseFisherTest — VariantWiseFisherTest","text":"variants_list List fraction values. n_cores Number cores want use. Numeric. p_value_adjustment Method P value adjustment. See p.adjust details. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/char_to_numeric.html","id":null,"dir":"Reference","previous_headings":"","what":"char_to_numeric — char_to_numeric","title":"char_to_numeric — char_to_numeric","text":"function convert heterozygous/homozygous information VCF consensus information VarTrix. used LoadingVCF_typewise.R.","code":""},{"path":"https://costalab.github.io/sigurd/reference/char_to_numeric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"char_to_numeric — char_to_numeric","text":"","code":"char_to_numeric(char_value)"},{"path":"https://costalab.github.io/sigurd/reference/char_to_numeric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"char_to_numeric — char_to_numeric","text":"char_value genotype encoding want convert?","code":""},{"path":"https://costalab.github.io/sigurd/reference/combine_NAMES.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_NAMES — combine_NAMES","title":"combine_NAMES — combine_NAMES","text":"combine two vectors names.","code":""},{"path":"https://costalab.github.io/sigurd/reference/combine_NAMES.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_NAMES — combine_NAMES","text":"","code":"combine_NAMES(x, y)"},{"path":"https://costalab.github.io/sigurd/reference/combine_NAMES.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combine_NAMES — combine_NAMES","text":"x First vector names. y Second vector names.","code":""},{"path":"https://costalab.github.io/sigurd/reference/combine_SparseMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_sparseMatrix — combine_SparseMatrix","title":"combine_sparseMatrix — combine_SparseMatrix","text":"combine two sparse matrices","code":""},{"path":"https://costalab.github.io/sigurd/reference/combine_SparseMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_sparseMatrix — combine_SparseMatrix","text":"","code":"combine_SparseMatrix(matrix_1, matrix_2)"},{"path":"https://costalab.github.io/sigurd/reference/combine_SparseMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combine_sparseMatrix — combine_SparseMatrix","text":"matrix_1 first sparse matrix. matrix_2 second matrix.","code":""},{"path":"https://costalab.github.io/sigurd/reference/computeAFMutMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"computeAFMutMatrix — computeAFMutMatrix","title":"computeAFMutMatrix — computeAFMutMatrix","text":"Calculate allele frequency per variant. Source: https://github.com/petervangalen/MAESTER-2021 can get AF values greater 1, due uninformative reads. See: https://gatk.broadinstitute.org/hc/en-us/articles/360035532252-Allele-Depth-AD--lower--expected https://github.com/caleblareau/mgatk/issues/1 simply set values 1, since actual information case.","code":""},{"path":"https://costalab.github.io/sigurd/reference/computeAFMutMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"computeAFMutMatrix — computeAFMutMatrix","text":"","code":"computeAFMutMatrix(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/computeAFMutMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"computeAFMutMatrix — computeAFMutMatrix","text":"SE SummarizedExperiment object. chromosome_prefix prefix chromosome.","code":""},{"path":"https://costalab.github.io/sigurd/reference/getAltMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"getAltMatrix — getAltMatrix","title":"getAltMatrix — getAltMatrix","text":"get alt values MAEGATK results. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/getAltMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getAltMatrix — getAltMatrix","text":"","code":"getAltMatrix(SE_object, letter, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/getAltMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getAltMatrix — getAltMatrix","text":"SE_object SummarizedExperiment object. letter base want use. Character. chromosome_prefix chromosome prefix used.","code":""},{"path":"https://costalab.github.io/sigurd/reference/getMutMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"getMutMatrix — getMutMatrix","title":"getMutMatrix — getMutMatrix","text":"function gets allele frequency specific allele. used computeAFMutMatrix. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/getMutMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getMutMatrix — getMutMatrix","text":"","code":"getMutMatrix(SE, cov, letter, ref_allele, chromosome_prefix)"},{"path":"https://costalab.github.io/sigurd/reference/getMutMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getMutMatrix — getMutMatrix","text":"SE SummarizedExperiment object. cov coverage matrix MAEGATK/MGATK. letter base interested . ref_allele Vector reference alleles. chromosome_prefix chromosome prefix used.","code":""},{"path":"https://costalab.github.io/sigurd/reference/getReadMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the counts for a specific base over all positions. — getReadMatrix","title":"Get the counts for a specific base over all positions. — getReadMatrix","text":"Get counts specific base positions.","code":""},{"path":"https://costalab.github.io/sigurd/reference/getReadMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the counts for a specific base over all positions. — getReadMatrix","text":"","code":"getReadMatrix(SE, letter, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/getReadMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the counts for a specific base over all positions. — getReadMatrix","text":"SE SummarizedExperiment object. letter base want counts. chromosome_prefix chromosome name used prefix.","code":""},{"path":"https://costalab.github.io/sigurd/reference/getRefMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"getRefMatrix — getRefMatrix","title":"getRefMatrix — getRefMatrix","text":"get reference values MAEGATK result. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/getRefMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getRefMatrix — getRefMatrix","text":"","code":"getRefMatrix(SE_object, letter, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/getRefMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getRefMatrix — getRefMatrix","text":"SE_object SummarizedExperiment object. letter base analysing. get matrix shows cells many reference reads letter. chromosome_prefix chromosome prefix used.","code":""},{"path":"https://costalab.github.io/sigurd/reference/get_consensus.html","id":null,"dir":"Reference","previous_headings":"","what":"get_consensus — get_consensus","title":"get_consensus — get_consensus","text":"get consensus information specific matrix. want remove packages needed. See package apperantly needed.","code":""},{"path":"https://costalab.github.io/sigurd/reference/get_consensus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_consensus — get_consensus","text":"","code":"get_consensus(alt_base, ref_base, input_matrix, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/get_consensus.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_consensus — get_consensus","text":"alt_base alternative base. ref_base reference base. input_matrix Input matrix present reads numerically encoded. chromosome_prefix chromosome name used prefix.","code":""},{"path":"https://costalab.github.io/sigurd/reference/ggsci_pal.html","id":null,"dir":"Reference","previous_headings":"","what":"ggsci_pal — ggsci_pal","title":"ggsci_pal — ggsci_pal","text":"Function return colours ggsci palette.","code":""},{"path":"https://costalab.github.io/sigurd/reference/ggsci_pal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ggsci_pal — ggsci_pal","text":"","code":"ggsci_pal(option, ...)"},{"path":"https://costalab.github.io/sigurd/reference/ggsci_pal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ggsci_pal — ggsci_pal","text":"option colour palette choice. ... options passed palette function.","code":""},{"path":"https://costalab.github.io/sigurd/reference/ggsci_pal.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"ggsci_pal — ggsci_pal","text":"function returns colour palette ggsci. Options : aaas: 10 d3: 10 futurama: 12 gsea: 12 igv: 51 jama: 7 jco: 10 npg: 10 lancet: 9  locuszoom: 7 material: 10 nejm: 8  rickandmorty: 12 simpsons: 16  startrek: 7 tron: 7 uchicago: 9  ucscgb: 26","code":""},{"path":"https://costalab.github.io/sigurd/reference/load_object.html","id":null,"dir":"Reference","previous_headings":"","what":"load_object — load_object","title":"load_object — load_object","text":"loading function load RDS files quicker. Source: https://github.com/CostaLab/CimpleG","code":""},{"path":"https://costalab.github.io/sigurd/reference/load_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"load_object — load_object","text":"","code":"load_object(file_name)"},{"path":"https://costalab.github.io/sigurd/reference/load_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"load_object — load_object","text":"file_name path file.","code":""},{"path":"https://costalab.github.io/sigurd/reference/save_object.html","id":null,"dir":"Reference","previous_headings":"","what":"save_object — save_object","title":"save_object — save_object","text":"Saving function save RDS files quicker. Source:https://github.com/CostaLab/CimpleG","code":""},{"path":"https://costalab.github.io/sigurd/reference/save_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"save_object — save_object","text":"","code":"save_object(object, file_name, file_format = \"zstd\")"},{"path":"https://costalab.github.io/sigurd/reference/save_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"save_object — save_object","text":"object R object save. file_name path file shall save. file_format format save file. one : zstd, lz4, gzip, bzip2, xz, nocomp.","code":""},{"path":"https://costalab.github.io/sigurd/reference/sdiv.html","id":null,"dir":"Reference","previous_headings":"","what":"Division of sparse matrix. — sdiv","title":"Division of sparse matrix. — sdiv","text":"Division sparse matrix.","code":""},{"path":"https://costalab.github.io/sigurd/reference/sdiv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Division of sparse matrix. — sdiv","text":"","code":"sdiv(X, Y, names = dimnames(X))"},{"path":"https://costalab.github.io/sigurd/reference/sdiv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Division of sparse matrix. — sdiv","text":"X First sparse matrix. Y Second sparse matrix. names dimension names (dimnames(X)).","code":""}]
+[{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"analysis-of-blastic-plasmacytoid-dendritic-cell-neoplasm-bpdcn","dir":"Articles","previous_headings":"","what":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":", compare analysis cells patient BPDCN. original script available : https://github.com/petervangalen/MAESTER-2021/blob/main/4_CH_sample/4.2_Variant_Selection.R setup, cells single donor separated categories. small clones might characterize clonal lineages sample selected.","code":""},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"loading-necessary-packages-","dir":"Articles","previous_headings":"","what":"Loading necessary packages.","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"load data MAESTER.","code":"print(\"Libraries for SIGURD.\") ## [1] \"Libraries for SIGURD.\" suppressPackageStartupMessages(library(sigurd)) suppressPackageStartupMessages(library(SummarizedExperiment)) suppressPackageStartupMessages(library(ggplot2))"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"loading-the-data-using-sigurd-","dir":"Articles","previous_headings":"","what":"Loading the data using SIGURD.","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"","code":"# The design matrix contains information for the genotyping data. genotyping <- LoadingMAEGATK_typewise(patient = \"BPDCN712\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv\", type_use = \"Amplicon_MT\", verbose = FALSE)  # Loading the scRNA-seq data. scrna <- readRDS(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/BPDCN712_Seurat_with_TCR_Renamed.rds\")"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"generating-a-block-list","dir":"Articles","previous_headings":"","what":"Generating a block list","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"Variants also detected cell mixture data treated possible false positives. used blacklist removed results.","code":"# Loading the TenX Cell Mixture Genotyping.  genotyping_tenx <- load_object(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/TenX_CellMixture_Genotyping.rds.lz4\") blocklist <- AllelFrequencyFoldChange(genotyping_tenx, group_of_interest = \"CellType\", group1 = \"K562\", group2 = \"BT142\", maximum_foldchange = 5, minimum_coverage = 5, minimum_allele_freq = 0.001, maximum_allele_freq = 0.999)$Variant  # We add the variant chrM_1583_A_G by hand. It is identified as misleading based on downstream analysis. blocklist <- c(blocklist, \"chrM_1583_A_G\")"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"selecting-the-variants-of-interest","dir":"Articles","previous_headings":"","what":"Selecting the Variants of Interest","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"Now, select variants interest loaded data.","code":"voi.ch.sigurd <- VariantSelection_TopCells(genotyping, min_coverage = 5, quantiles = 0.9, thresholds = 0, top_cells = 10, top_VAF = 0.5, min_quality = 30, remove_nocall = FALSE, verbose = FALSE) voi.ch.sigurd <- voi.ch.sigurd[!voi.ch.sigurd %in% blocklist] print(voi.ch.sigurd) ##  [1] \"chrM_683_G_A\"   \"chrM_1323_G_A\"  \"chrM_1415_G_A\"  \"chrM_2593_G_A\"  ##  [5] \"chrM_6205_G_A\"  \"chrM_6243_G_A\"  \"chrM_8697_G_A\"  \"chrM_9753_G_A\"  ##  [9] \"chrM_10158_T_A\" \"chrM_15140_G_A\" \"chrM_15812_G_A\" \"chrM_779_T_C\"   ## [13] \"chrM_3988_T_C\"  \"chrM_6185_T_C\"  \"chrM_6293_T_C\"  \"chrM_9164_T_C\"  ## [17] \"chrM_9321_T_C\"  \"chrM_11864_T_C\" \"chrM_15299_T_C\" \"chrM_1171_A_G\"  ## [21] \"chrM_1222_A_G\"  \"chrM_2241_A_G\"  \"chrM_2623_A_G\"  \"chrM_3628_A_G\"  ## [25] \"chrM_4104_A_G\"  \"chrM_6218_A_G\""},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"visualisation-using-sigurd","dir":"Articles","previous_headings":"","what":"Visualisation using SIGURD","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"","code":"genotyping <- Filtering(SE = genotyping, cells_include = colnames(scrna)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" colData(genotyping)$CellType <- scrna$CellType HeatmapVoi(SE = genotyping, voi = voi.ch.sigurd, annotation_trait = \"CellType\", sort_cells = TRUE, remove_empty_cells = TRUE, minimum_allele_freq = 0.01)"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"cell-type-enrichment-2593ga","dir":"Articles","previous_headings":"","what":"Cell Type Enrichment 2593G>A","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"check cell type enrichment variant 2593G>.","code":"result_enrichment <- Enrichment_FisherTest(se = genotyping, variant = \"chrM_2593_G_A\", use_nocall = FALSE, trait = \"CellType\") ## [1] \"We get a count matrix of the chrM_2593_G_A per CellType.\" ComplexHeatmap::Heatmap(as.matrix(result_enrichment$Heatmap_Values), cluster_rows = FALSE, cluster_columns = FALSE, col= circlize::colorRamp2(c(0, max(result_enrichment$Heatmap_Values, na.rm = TRUE)), c(\"white\", \"red\")))"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"cell-type-enrichment-6243ga","dir":"Articles","previous_headings":"","what":"Cell Type Enrichment 6243G>A","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"check cell type enrichment variant 6243G>.","code":"result_enrichment <- Enrichment_FisherTest(se = genotyping, variant = \"chrM_6243_G_A\", use_nocall = FALSE, trait = \"CellType\") ## [1] \"We get a count matrix of the chrM_6243_G_A per CellType.\" ComplexHeatmap::Heatmap(as.matrix(result_enrichment$Heatmap_Values), cluster_rows = FALSE, cluster_columns = FALSE, col= circlize::colorRamp2(c(0, max(result_enrichment$Heatmap_Values, na.rm = TRUE)), c(\"white\", \"red\")))"},{"path":"https://costalab.github.io/sigurd/articles/BoneMarrow_SIGURD.html","id":"enrichment-with-somatic-variants","dir":"Articles","previous_headings":"","what":"Enrichment with somatic variants","title":"Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)","text":"get number 2593_G>cells also mutated different somatic variant.","code":"somatic_variants <- c(\"ASXL1.G642fs.1\", \"ASXL1.G642fs.2\", \"TET2.S792X\", \"TET2.Q1034X\", \"TET2.R1216X\", \"TET2.H1380Y\") variants <- LoadingRawMatrix_typewise(samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv\", patient = \"BPDCN712\", variant_use = somatic_variants, matrix_column_separator = \"\\t\", verbose = FALSE) genotyping <- genotyping[voi.ch.sigurd, ] genotyping <- Filtering(genotyping, cells_include = colnames(variants)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" variants <- Filtering(variants, cells_include = colnames(scrna), fraction_threshold = 0.01, reject_value = \"Reference\") ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We assume that cells with a fraction smaller than our threshold are actually Reference.\" ## [1] \"We set consensus values to 1 (Reference) and fraction values to 0.\" ## [1] \"We do not set fractions between 0.01 and 1 to 1.\" ## [1] \"This way, we retain the heterozygous information.\" ## [1] \"We remove all the variants that are always NoCall.\" genotyping <- CombineSEobjects(se_1 = genotyping, se_2 = variants) genotyping <- ClonalDefinition(se = genotyping, variants_ls = list(\"chrM_2593_G_A\"), grouping = NULL, identities = NULL, explicit = TRUE, explicit_not = list(\"chrM_6243_G_A\"), explicit_min_vaf = 0.01, verbose = TRUE) ## [1] \"Explicit clone definition.\" genotyping <- genotyping[, genotyping$Clones == \"C1\"] res <- VariantWiseFisherTest(variants_list = RowWiseSplit(se = genotyping)) ## [1] \"Testing Variant: ASXL1.G642fs.1, 1 out of 6\" ## [1] \"Testing Variant: ASXL1.G642fs.2, 2 out of 6\" ## [1] \"Testing Variant: TET2.S792X, 3 out of 6\" ## [1] \"Testing Variant: TET2.Q1034X, 4 out of 6\" ## [1] \"Testing Variant: TET2.R1216X, 5 out of 6\" ## [1] \"Testing Variant: TET2.H1380Y, 6 out of 6\" ## [1] \"We remove the NA P values.\" ## [1] \"Adjusting P values using fdr.\" knitr::kable(res, format=\"html\")"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"loading-necessary-packages-","dir":"Articles","previous_headings":"","what":"Loading necessary packages.","title":"MPN SIGURD","text":"","code":"suppressPackageStartupMessages(library(sigurd)) suppressPackageStartupMessages(library(SummarizedExperiment)) suppressPackageStartupMessages(library(ggplot2)) suppressPackageStartupMessages(library(Seurat)) suppressPackageStartupMessages(library(ComplexHeatmap)) suppressPackageStartupMessages(library(circlize)) suppressPackageStartupMessages(library(grid)) suppressPackageStartupMessages(library(EnhancedVolcano))"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"analysis-of-mpn-data","dir":"Articles","previous_headings":"","what":"Analysis of MPN data","title":"MPN SIGURD","text":", illustrate analysis genotyping data MPN samples. JAK2V617F mutation genotyped 6 MPN samples 3 healthy controls. setup makes analysis different previous analyses. Previously, one sample analysed time. Now, load analyse samples simultaneously.","code":""},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"loading-mpn-data","dir":"Articles","previous_headings":"","what":"Loading MPN data","title":"MPN SIGURD","text":"Now, load JAK2V617F data plot mutated cells UMAP. Since loading multiple samples, code complicated code MAESTER SW sample.","code":"# Loading the scRNA-seq data. scrna <- load_object(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/scrna_MPN.rds.lz4\")  # Loading the genotyping data. genotyping  <- LoadingVarTrix_typewise(patient = \"MPN\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_VarTrix.csv\", min_reads = 0, vcf_path = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/CosmicSubset_JAK2V617F.vcf\", type_use = \"scRNAseq_Somatic\", min_cells = 0, verbose = FALSE) amplicon <- LoadingVarTrix_typewise(patient = \"MPN\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_Amplicon.csv\", min_reads = 0, vcf_path = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/CosmicSubset_UCSC_JAK2V617F.vcf\", type_use = \"scRNAseq_Amplicon\", min_cells = 0, verbose = FALSE) genotyping  <- AmpliconSupplementing(scRNAseq = genotyping, amplicon = amplicon, verbose = FALSE)  # Filtering the genotyping object to remove false positives. genotyping <- Filtering(genotyping, min_cells_per_variant = 0, fraction_threshold = 0.21, cells_include = colnames(scrna), min_variants_per_cell = 1, reject_value = \"NoCall\", verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"combining-seurat-and-sigurd","dir":"Articles","previous_headings":"","what":"Combining Seurat and SIGURD","title":"MPN SIGURD","text":"Now, add genotyping information Seurat object.","code":"scrna <- SetVariantInfo(SE = genotyping, seurat_object = scrna) ## [1] \"You did not supply a vector of variants. All variants will be used.\""},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"visualisation","dir":"Articles","previous_headings":"","what":"Visualisation","title":"MPN SIGURD","text":"visualise genotyping information UMAP.","code":"# Plotting the mutated cells on the UMAP. scrna$JAK2_p.V617F_c.1849G.T_consensus <- factor(scrna$JAK2_p.V617F_c.1849G.T_consensus, levels = c(\"Ref\", \"Alt\")) jak2_cells <- sum(scrna$JAK2_p.V617F_c.1849G.T_consensus == \"Alt\", na.rm = TRUE) ref_cells <- sum(scrna$JAK2_p.V617F_c.1849G.T_consensus == \"Ref\", na.rm = TRUE) all_cells <- ncol(scrna) p <- DimPlot(scrna, group.by = \"JAK2_p.V617F_c.1849G.T_consensus\", reduction = \"INTE_UMAP\", order = TRUE, pt.size = 1, raster = FALSE, na.value = \"grey95\", cols = c(Alt = \"#aa0051\", Ref = \"#79b938\")) +   ggtitle(paste0(\"Alt: \", jak2_cells, \", Ref: \", ref_cells, \", All: \", all_cells)) +   xlab(\"UMAP 1\") + ylab(\"UMAP 2\") + scale_color_manual(breaks = c(\"Alt\", \"Ref\"), values = c(\"#aa0051\", \"#79b938\"), na.value = \"grey95\") +   theme(legend.position = \"top\") ## Scale for colour is already present. ## Adding another scale for colour, which will replace the existing scale. print(p)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"we-determine-degs-between-the-jak2v617f-and-wt-cells-","dir":"Articles","previous_headings":"","what":"We determine DEGs between the JAK2V617F and WT cells.","title":"MPN SIGURD","text":"Now, determine DEGs JAK2V617F cells wild type cells Orthochromatic Erythroblasts.","code":"scrna_orthoe <- subset(scrna, CellType == \"Orthochromatic Erythroblasts\" & Condition != \"HC\") degs <- FindMarkers(scrna_orthoe, group.by = \"JAK2_p.V617F_c.1849G.T_consensus\", ident.1 = \"Alt\", ident.2 = \"Ref\", logfc.threshold = 0) degs <- data.frame(degs, gene = rownames(degs)) degs_up   <- nrow(subset(degs, avg_log2FC >   0.25 & p_val_adj < 0.05)) degs_down <- nrow(subset(degs, avg_log2FC <  -0.25 & p_val_adj < 0.05)) EnhancedVolcano(degs, x = \"avg_log2FC\", y = \"p_val_adj\", lab = degs$gene, FCcutoff = 0.25, pCutoff = 0.05, title = \"OrthoE JAK2V617F Pos. vs. Neg.\",subtitle = NULL)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"combining-the-jak2v617f-data-with-the-mt-data-","dir":"Articles","previous_headings":"","what":"Combining the JAK2V617F data with the MT data.","title":"MPN SIGURD","text":"combine JAK2V617F SIGURD object MT object. Cells variants objects combined. save time, processing single sample. samples processed equally. Since genotyping object list, easily processed using parallel computing. First, load filter mitochondrial variant information.","code":"# Loading the data.  genotyping_mt <- LoadingMAEGATK_typewise(patient = \"MPN1\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_MT.csv\", min_cells = 0, cells_include = colnames(scrna), type_use = \"scRNAseq_MT\", verbose = FALSE) genotyping_mt <- Filtering(genotyping_mt, min_variants_per_cell = 1, min_cells_per_variant = 2, fraction_threshold = 0.05, cells_include = colnames(scrna), verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"mpn-vois-and-diversity","dir":"Articles","previous_headings":"","what":"MPN VOIs and Diversity","title":"MPN SIGURD","text":"Now, select mtVOIs. determine clonal lineages plot results heatmap. subset cells include erythroid cells.","code":"# Subset to erythroid cells. erythroid_cells <- subset(scrna, annotation == \"ErythroidCells\") genotyping_mt <- Filtering(genotyping_mt, cells_include = colnames(erythroid_cells)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" # Selecting the mtVOIS. mt_vois <- VariantSelection_Quantile(genotyping_mt, min_coverage = 1, verbose = FALSE)  # Determining the clonal lineages. genotyping_mt <- ClonalDefinition(se = genotyping_mt, variants_ls = list(mt_vois), verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"visualisation-of-mtvois-and-clonal-lineages","dir":"Articles","previous_headings":"","what":"Visualisation of mtVOIs and Clonal Lineages","title":"MPN SIGURD","text":"now plot variants interest clonal lineages.","code":"# Generating a heatmap. colors_lineage <- c(\"C1\" = \"#563e00\", \"C2\" = \"#dec234\", \"C3\" = \"#e23856\", \"C4\" = \"#7f0073\", \"C5\" = \"#006639\", \"C6\" = \"#b1db8e\", \"C7\" = \"#00348f\", \"Negative\" = \"black\") ha <- columnAnnotation(Clones = colData(genotyping_mt)[,\"Clones\"],                        col = list(Clones = colors_lineage),                        annotation_name_gp = gpar(fontsize = 10, fontface = \"plain\"),                        annotation_legend_param = list(Clones = list(nrow = 1, title = \"\"))) fraction <- as.matrix(assays(genotyping_mt)[[\"fraction\"]])[mt_vois, ] hm <- Heatmap(fraction,   name = \"VAF\",   row_title_gp = gpar(fontsize = 12),   row_names_gp = gpar(fontsize = 10),   row_names_max_width = unit(16, \"cm\"),   column_title = \"MPN1\",   column_title_gp = gpar(fontsize = 12),   column_names_gp = gpar(fontsize = 10),   col = colorRamp2(seq(0, round(max(fraction, na.rm = TRUE)), length.out = 9), c(\"#FCFCFC\", \"#FFEDB0\", \"#FFDF5F\", \"#FEC510\", \"#FA8E24\", \"#F14C2B\", \"#DA2828\", \"#BE2222\", \"#A31D1D\")),   show_column_dend = FALSE,   show_row_names = TRUE,   show_column_names = FALSE,   cluster_columns = TRUE,   cluster_rows = FALSE,   heatmap_legend_param = list(border = \"#000000\", grid_height = unit(10, \"mm\"),   direction = \"horizontal\"),   bottom_annotation = ha,   border = TRUE,   use_raster = TRUE,   show_heatmap_legend = TRUE) draw(hm, annotation_legend_side = \"bottom\")"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"calculating-clonal-diversity-","dir":"Articles","previous_headings":"","what":"Calculating clonal diversity.","title":"MPN SIGURD","text":"calculate clonal diversity sample MPN1 example.","code":"clonal_diversity <- ClonalDiversity(genotyping_mt, grouping = \"Clones\", diversity_measure = \"EffectiveSpecies\", verbose = FALSE) print(paste0(\"Clonal Diversity in Effective Number of Species for MPN1: \", clonal_diversity)) ## [1] \"Clonal Diversity in Effective Number of Species for MPN1: 6.72545022391521\""},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"repeating-the-mt-analysis-for-all-samples-","dir":"Articles","previous_headings":"","what":"Repeating the MT analysis for all samples.","title":"MPN SIGURD","text":"now repeat MT analysis samples. take considereable time. speed analsyis using parallel computing. load results generated code.","code":"# We get all patients present in the design matrix. design_matrix <- read.table(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_MT.csv\", header = TRUE, sep = \",\") patients <- design_matrix$patient[1] genotyping_mt_all <- parallel::mclapply(patients, LoadingMAEGATK_typewise, samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/DesignMatrix_MT.csv\", min_cells = 0, cells_include = colnames(scrna), type_use = \"scRNAseq_MT\", verbose = FALSE, mc.cores = length(patients)) names(genotyping_mt_all) <- patients genotyping_mt_all <- parallel::mclapply(genotyping_mt_all, Filtering, min_variants_per_cell = 1, min_cells_per_variant = 2, fraction_threshold = 0.05, cells_include = colnames(scrna), verbose = FALSE, mc.cores = length(patients))"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"selecting-variants-of-interest-for-all-samples","dir":"Articles","previous_headings":"","what":"Selecting variants of interest for all samples","title":"MPN SIGURD","text":"select variants interest samples.","code":"# Selecting the mtVOIS. mt_vois_all <- parallel::mclapply(genotyping_mt_all, VariantSelection_Quantile, min_coverage = 1, verbose = FALSE, mc.cores = length(patients))  # Determining the clonal lineages. This takes very long. We use parallel computing to process all samples simultaneously. genotyping_mt_all <- parallel::mclapply(1:length(mt_vois_all), function(x){   sample_use <- names(mt_vois_all)[x]   clones <- sigurd::ClonalDefinition(se = genotyping_mt_all[[sample_use]], mt_vois_all[sample_use], verbose = FALSE)   return(clones) }, mc.cores = length(mt_vois_all)) names(genotyping_mt_all) <- patients save_object(genotyping_mt_all, \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/genotyping_mt_all.rds.lz4\", \"lz4\")"},{"path":"https://costalab.github.io/sigurd/articles/MPN_SIGURD.html","id":"calculating-the-diverstiy-for-all-samples","dir":"Articles","previous_headings":"","what":"Calculating the diverstiy for all samples","title":"MPN SIGURD","text":"","code":"# We load the previous results. genotyping_mt_all <- load_object(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/genotyping_mt_all.rds.lz4\") clonal_diversity_all <- unlist(lapply(genotyping_mt_all, ClonalDiversity, grouping = \"Clones\", diversity_measure = \"EffectiveSpecies\", verbose = FALSE)) clonal_diversity_all <- data.frame(Sample = names(genotyping_mt_all), EffectiveSpecies = clonal_diversity_all) knitr::kable(clonal_diversity_all, format=\"html\")"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"cell-mixture-analysis-using-sigurd","dir":"Articles","previous_headings":"","what":"Cell Mixture Analysis using SIGURD","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"data set, chronic myelogenous leukemia cells (K562) brain tumor cells (BT142) mixed sequenced using Seq-Well S3. cells can separated using expression marker genes. original script identifies 6 variants can distinguish two cell types. reproduction, show analysis can faithfully reproduced using streamlined set functions. greatly simplifies analysis. Using set dedicated functions, analysis can now also easily adopted new data sets.","code":""},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"loading-necessary-packages-","dir":"Articles","previous_headings":"","what":"Loading necessary packages.","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"load data MAESTER.","code":"print(\"Libraries for SIGURD.\") ## [1] \"Libraries for SIGURD.\" suppressPackageStartupMessages(library(sigurd)) suppressPackageStartupMessages(library(SummarizedExperiment)) suppressPackageStartupMessages(library(ggplot2))"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"we-load-the-seurat-object-for-the-scrna-seq-data-","dir":"Articles","previous_headings":"","what":"We load the Seurat object for the scRNA-seq data.","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"","code":"seu <- readRDS(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/SW_CellLineMix_Seurat_Keep_Renamed.rds\")"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"loading-the-data-using-sigurd-","dir":"Articles","previous_headings":"","what":"Loading the data using SIGURD.","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"SIGURD loads data automatically reformats data. code uses dedicated functions load process data, streamlines analysis quite substantially.","code":"# The design matrix contains information for the genotyping data. genotyping <- LoadingMAEGATK_typewise(patient = \"SW\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv\", min_cells = 0, type_use = \"Amplicon_MT\", verbose = FALSE)  # Removing cells that are not in the Seurat object. genotyping <- Filtering(genotyping, cells_include = colnames(seu)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" # Adding meta data do the SIGURD object. colData(genotyping)$CellType <- seu$CellType"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"selecting-the-variants-of-interest","dir":"Articles","previous_headings":"","what":"Selecting the Variants of Interest","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"Now, select variants interest.","code":"# Selecting informative variants.  voi.ch.sigurd <- VariantSelection_Quantile(genotyping, min_coverage = 20, min_quality = 30, quantiles = c(0.1, 0.9), thresholds = c(0.1, 0.9), verbose = FALSE) print(voi.ch.sigurd) ## [1] \"chrM_709_G_A\"  \"chrM_1888_G_A\" \"chrM_1420_T_C\" \"chrM_2141_T_C\" ## [5] \"chrM_9117_T_C\" \"chrM_7990_C_T\""},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"visualisation-using-sigurd","dir":"Articles","previous_headings":"","what":"Visualisation using SIGURD","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"","code":"# Determining if a cell is supporting one of the two cell types. cell_support <- CallSupport(SE = genotyping, VOI_group1 = voi.ch.sigurd[voi.ch.sigurd != \"chrM_7990_C_T\"], VOI_group2 = \"chrM_7990_C_T\", group1_name = \"K562\", group2_name = \"BT142\", min_mutated_reads = 3, min_reads = 30, group_factor = 10, verbose = FALSE, return_nonsupport = TRUE) colData(genotyping)$CellType_MT <- cell_support$Support cell_support <- subset(cell_support, Support %in% c(\"K562\", \"BT142\")) # Selecting only cells with sufficient support for a set of variants.  # Plotting the results on a heatmap. HeatmapVoi(SE = genotyping[,cell_support$Cell], voi = voi.ch.sigurd, annotation_trait = \"CellType\", minimum_coverage = 3, remove_empty_cells = FALSE)"},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"selecting-variants-with-comparatively-high-vaf-between-groups","dir":"Articles","previous_headings":"","what":"Selecting variants with comparatively high VAF between groups","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"now select variants higher VAF K562 cells BT142 cells.","code":"voi.ch.lineages <- sigurd::VariantSelection_Group(SE = genotyping, min_coverage = 20, quantiles = c(0.01, 0.99), thresholds = c(0.01, 0.02), min_quality = 30,                                                   group_of_interest = \"CellType_MT\", group1 = \"K562\", group2 = \"BT142\", group_factor = 5, remove_nocall = FALSE, verbose = FALSE) voi.ch.lineages <- gsub(\"chrM_9117_T_C\", \"chrM_2141_T_C\", voi.ch.lineages) # Replace chrM_9117_T_C, which comes up because it has no coverage in some cells, with another homoplasmic variant (chrM_2141_T_C), that has better coverage) voi.ch.lineages <- voi.ch.lineages[!voi.ch.lineages %in% c(\"chrM_5378_A_G\", \"chrM_6384_G_A\")] # These variants are not detected in the bulk data and were removed by hand. print(voi.ch.lineages) ##  [1] \"chrM_1197_G_A\" \"chrM_1227_G_A\" \"chrM_1327_G_A\" \"chrM_1982_G_A\" ##  [5] \"chrM_2008_G_A\" \"chrM_2147_G_A\" \"chrM_2170_G_A\" \"chrM_2478_G_A\" ##  [9] \"chrM_2571_G_A\" \"chrM_2573_G_A\" \"chrM_2810_G_A\" \"chrM_2943_G_A\" ## [13] \"chrM_5274_G_A\" \"chrM_8155_G_A\" \"chrM_8213_G_A\" \"chrM_8278_C_A\" ## [17] \"chrM_9778_G_A\" \"chrM_2141_T_C\" \"chrM_1310_C_T\" \"chrM_1352_C_T\" ## [21] \"chrM_1533_C_T\" \"chrM_9757_C_T\""},{"path":"https://costalab.github.io/sigurd/articles/SW_CellMixture_SIGURD.html","id":"visualisation-using-sigurd-1","dir":"Articles","previous_headings":"","what":"Visualisation using SIGURD","title":"Cell Mixture Analysis using Seq-Well Sequencing","text":"","code":"# Plotting the results on a heatmap. cell_support <- subset(cell_support, Support == \"K562\") genotyping <- Filtering(genotyping, cells_include = cell_support$Cell, verbose = FALSE) HeatmapVoi(SE = genotyping, voi = voi.ch.lineages, minimum_coverage = 3, sort_cells = TRUE, cluster_variants = TRUE)"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"cell-mixture-experiment-using-10x-genomics-sequencing","dir":"Articles","previous_headings":"","what":"Cell Mixture Experiment using 10X Genomics Sequencing","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":", reproduce analysis cell mixture experiment.","code":""},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"loading-necessary-packages-","dir":"Articles","previous_headings":"","what":"Loading necessary packages.","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"load data MAESTER.","code":"print(\"Libraries for SIGURD.\") ## [1] \"Libraries for SIGURD.\" suppressPackageStartupMessages(library(sigurd)) suppressPackageStartupMessages(library(SummarizedExperiment)) suppressPackageStartupMessages(library(ggplot2))"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"we-load-the-seurat-object-for-the-scrna-seq-data-","dir":"Articles","previous_headings":"","what":"We load the Seurat object for the scRNA-seq data.","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"","code":"seu <- readRDS(\"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/TenX_CellLineMix_Seurat_Keep_Renamed.rds\")"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"loading-the-data-using-sigurd-","dir":"Articles","previous_headings":"","what":"Loading the data using SIGURD.","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"","code":"# The design matrix contains information for the genotyping data. genotyping <- LoadingMAEGATK_typewise(patient = \"TenX\", samples_file = \"/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv\", min_cells = 0, type_use = \"Amplicon_MT\", verbose = FALSE)  # Removing cells that are not in the Seurat object. genotyping <- Filtering(genotyping, cells_include = colnames(seu)) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" # Adding meta data do the SIGURD object. colData(genotyping)$CellType <- seu$CellType"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"selecting-the-variants-of-interest","dir":"Articles","previous_headings":"","what":"Selecting the Variants of Interest","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"","code":"# Selecting informative variants.  voi.ch.sigurd <- VariantSelection_Quantile(genotyping, min_coverage = 20, min_quality = 30, quantiles = c(0.1, 0.9), thresholds = c(0.1, 0.9), verbose = FALSE) print(voi.ch.sigurd) ##  [1] \"chrM_709_G_A\"   \"chrM_1888_G_A\"  \"chrM_6249_G_A\"  \"chrM_8697_G_A\"  ##  [5] \"chrM_11719_G_A\" \"chrM_15452_C_A\" \"chrM_1420_T_C\"  \"chrM_2141_T_C\"  ##  [9] \"chrM_4216_T_C\"  \"chrM_6524_T_C\"  \"chrM_9117_T_C\"  \"chrM_11251_A_G\" ## [13] \"chrM_11764_A_G\" \"chrM_11812_A_G\" \"chrM_15607_A_G\" \"chrM_7990_C_T\"  ## [17] \"chrM_12741_C_T\""},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"visualisation-using-sigurd","dir":"Articles","previous_headings":"","what":"Visualisation using SIGURD","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"","code":"# Determining if a cell is supporting one of the two cell types. cell_support <- CallSupport(SE = genotyping, VOI_group1 = voi.ch.sigurd[voi.ch.sigurd != \"chrM_7990_C_T\"], VOI_group2 = \"chrM_7990_C_T\", group1_name = \"K562\", group2_name = \"BT142\", min_mutated_reads = 3, min_reads = 30, group_factor = c(10,2), verbose = FALSE) genotyping <- Filtering(genotyping, cells_include = cell_support$Cell) ## [1] \"We remove all cells not in the allow list.\" ## [1] \"We remove all the variants that are always NoCall.\" colData(genotyping)$CellType_MT <- cell_support$Support cell_support <- subset(cell_support, Support %in% c(\"K562\", \"BT142\")) # Selecting only cells with sufficient support for a set of variants.  # Plotting the results on a heatmap. HeatmapVoi(SE = genotyping, voi = voi.ch.sigurd, annotation_trait = \"CellType\", minimum_coverage = 3)"},{"path":"https://costalab.github.io/sigurd/articles/TenX_CellMixture_SIGURD.html","id":"selecting-variants-with-comparatively-high-vaf-between-groups","dir":"Articles","previous_headings":"","what":"Selecting variants with comparatively high VAF between groups","title":"Cell Mixture Experiment using 10X Genomics Sequencing","text":"now select variants higher VAF K562 cells BT142 cells.","code":"voi.ch.lineages <- sigurd::VariantSelection_Group(SE = genotyping, min_coverage = 100, quantiles = c(0.01, 0.99), thresholds = c(0.01, 0.02), min_quality = 30,                                                   group_of_interest = \"CellType_MT\", group1 = \"K562\", group2 = \"BT142\", group_factor = 5, remove_nocall = FALSE, verbose = FALSE) voi.ch.lineages <- voi.ch.lineages[!voi.ch.lineages %in% c(\"chrM_8251_G_A\", \"chrM_7693_C_T\")] # These variants are not detected in the bulk data and were removed by hand. voi.ch.lineages <- c(voi.ch.lineages, \"chrM_2141_T_C\") # Adding a homoplasmic variant as positive control. print(voi.ch.lineages) ##  [1] \"chrM_1916_G_A\"  \"chrM_2008_G_A\"  \"chrM_2147_G_A\"  \"chrM_2551_G_A\"  ##  [5] \"chrM_2571_G_A\"  \"chrM_2573_G_A\"  \"chrM_7269_G_A\"  \"chrM_7337_G_A\"  ##  [9] \"chrM_7362_G_A\"  \"chrM_7706_G_A\"  \"chrM_8155_G_A\"  \"chrM_9247_G_A\"  ## [13] \"chrM_9778_G_A\"  \"chrM_10223_C_A\" \"chrM_11531_G_A\" \"chrM_11914_G_A\" ## [17] \"chrM_15374_G_A\" \"chrM_8211_T_C\"  \"chrM_9613_T_C\"  \"chrM_1733_C_T\"  ## [21] \"chrM_2357_C_T\"  \"chrM_2574_G_T\"  \"chrM_7825_C_T\"  \"chrM_9757_C_T\"  ## [25] \"chrM_9822_C_T\"  \"chrM_11965_C_T\" \"chrM_12102_C_T\" \"chrM_2141_T_C\" # Plotting the results on a heatmap. cell_support <- subset(cell_support, Support == \"K562\") # Only plotting K562 cells. genotyping <- Filtering(genotyping, cells_include = cell_support$Cell, verbose = FALSE) HeatmapVoi(SE = genotyping, voi = voi.ch.lineages, minimum_coverage = 3, sort_cells = TRUE, cluster_variants = TRUE)"},{"path":"https://costalab.github.io/sigurd/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Martin Grasshoff. Author, maintainer. Ivan Costa. Author.","code":""},{"path":"https://costalab.github.io/sigurd/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Grasshoff M, Costa (2024). sigurd: Single cell Genotyping Using RNA Data. R package version 0.3.1, https://costalab.github.io/sigurd/.","code":"@Manual{,   title = {sigurd: Single cell Genotyping Using RNA Data},   author = {Martin Grasshoff and Ivan Costa},   year = {2024},   note = {R package version 0.3.1},   url = {https://costalab.github.io/sigurd/}, }"},{"path":"https://costalab.github.io/sigurd/index.html","id":"single-cell-genotyping-using-rna-data-sigurd","dir":"","previous_headings":"","what":"Single cell Genotyping Using RNA Data","title":"Single cell Genotyping Using RNA Data","text":"Martin Graßhoff1 Ivan G. Costa1 1Institute Computational Genomics, Faculty Medicine, RWTH Aachen University, Aachen, 52074 Germany Motivation: advent single RNA seq assays, became possible determine mutational status individual cell. Single cell RNA seq data nature sparse probability hitting specific variants interest therefore low. issue can overcome using modified amplicon assays, also possible impute mutational status using correlation detected mitochondrial somatic variants. Results: Sigurd R package analysis single cell data. determine overall variant burden per cell also number interesting mitochondrial variants using previously published approaches. employ imputation approach utilizes correlation mitochondrial variants somatic variants. Mitochondrial mutations significantly associated somatic mutations used stand-ins.","code":""},{"path":"https://costalab.github.io/sigurd/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Single cell Genotyping Using RNA Data","text":"can install sigurd using following code. vignette requires data currently published, provided reference.","code":"install.packages(\"devtools\") devtools::install_github(\"https://github.com/CostaLab/sigurd.git\", build_vignettes = FALSE) require(sigurd)"},{"path":"https://costalab.github.io/sigurd/index.html","id":"sigurd","dir":"","previous_headings":"","what":"SIGURD","title":"Single cell Genotyping Using RNA Data","text":"provided small example data set SiGURD. consists chromosome 9 MT one MPN sample. mutation data obtained Sanger Institute Catalogue Somatic Mutations Cancer web site, http://cancer.sanger.ac.uk/cosmic Bamford et al (2004) COSMIC (Catalogue Somatic Mutations Cancer) database website. Br J Cancer, 91,355-358.","code":"# This will be included for published data. # vignette('sigurd')"},{"path":"https://costalab.github.io/sigurd/index.html","id":"current-features-v0-3-1","dir":"","previous_headings":"","what":"Current Features v0.3.1","title":"Single cell Genotyping Using RNA Data","text":"Loading data VarTrix MAEGATK. Transforming data compatible joint analysis. Calculating variant burden per cell. Thresholding variants using approach described Miller et al. [2] Finding associated variants using correlation Fisher Test.","code":""},{"path":"https://costalab.github.io/sigurd/index.html","id":"sources","dir":"","previous_headings":"","what":"Sources","title":"Single cell Genotyping Using RNA Data","text":"package implements approaches following packages respositories: - https://github.com/petervangalen/MAESTER-2021 – Variant Thresholding functions loading MAEGATK data. - https://github.com/CostaLab/CimpleG – loading saving function.","code":""},{"path":"https://costalab.github.io/sigurd/index.html","id":"future","dir":"","previous_headings":"","what":"Future","title":"Single cell Genotyping Using RNA Data","text":"Memory optimization Loading CB sniffer results Providing data vignette","code":""},{"path":"https://costalab.github.io/sigurd/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"Single cell Genotyping Using RNA Data","text":"[1] VarTrix. github [2] Miller, T.E., et al. Mitochondrial variant enrichment high-throughput single-cell RNA sequencing resolves clonal populations. Nat Biotechnol (2022). link. See also: MAEGATK Analysis, Data","code":""},{"path":"https://costalab.github.io/sigurd/reference/AllelFrequencyFoldChange.html","id":null,"dir":"Reference","previous_headings":"","what":"AllelFrequencyFoldChange — AllelFrequencyFoldChange","title":"AllelFrequencyFoldChange — AllelFrequencyFoldChange","text":"Check cell supported set variants.","code":""},{"path":"https://costalab.github.io/sigurd/reference/AllelFrequencyFoldChange.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"AllelFrequencyFoldChange — AllelFrequencyFoldChange","text":"","code":"AllelFrequencyFoldChange(   SE,   VOI = NULL,   group_of_interest,   group1 = \"group1\",   group2 = \"group2\",   maximum_foldchange = NULL,   minimum_foldchange = NULL,   minimum_coverage = NULL,   minimum_allele_freq = NULL,   maximum_allele_freq = NULL,   verbose = FALSE )"},{"path":"https://costalab.github.io/sigurd/reference/AllelFrequencyFoldChange.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"AllelFrequencyFoldChange — AllelFrequencyFoldChange","text":"SE SummarizedExperiment object. VOI variants variants analyzed. NULL used. group_of_interest column data divides cells. group1 first group. group2 second group. maximum_foldchange Maximum fold change. minimum_foldchange Minimum fold change. minimum_coverage Minimum coverage variant. minimum_allele_freq Minimum allele frequency groups. maximum_allele_freq Maximum allele frequency groups. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing.html","id":null,"dir":"Reference","previous_headings":"","what":"Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing","title":"Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing","text":"replace values scRNAseq experiment values amplicon experiment.","code":""},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing","text":"","code":"AmpliconSupplementing(scRNAseq, amplicon, verbose = TRUE)"},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Supplementing scRNAseq values with Amplicon values — AmpliconSupplementing","text":"scRNAseq SummarizedExperiment object containing scRNAseq data. amplicon SummarizedExperiment object containing amplicon data. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing_big.html","id":null,"dir":"Reference","previous_headings":"","what":"Supplementing scRNAseq values with Amplicon values using big.matrix — AmpliconSupplementing_big","title":"Supplementing scRNAseq values with Amplicon values using big.matrix — AmpliconSupplementing_big","text":"replace values scRNAseq experiment values amplicon experiment.","code":""},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supplementing scRNAseq values with Amplicon values using big.matrix — AmpliconSupplementing_big","text":"","code":"AmpliconSupplementing_big(scRNAseq, amplicon)"},{"path":"https://costalab.github.io/sigurd/reference/AmpliconSupplementing_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Supplementing scRNAseq values with Amplicon values using big.matrix — AmpliconSupplementing_big","text":"scRNAseq SummarizedExperiment object containing scRNAseq data. amplicon SummarizedExperiment object containing amplicon data.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateAlleleFrequency.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculating the Minor Allele Frequency. — CalculateAlleleFrequency","title":"Calculating the Minor Allele Frequency. — CalculateAlleleFrequency","text":"calculate MAF reference reads matrix alternative reads matrix. function intended used mitochondrial genome somatic mutations.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateAlleleFrequency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculating the Minor Allele Frequency. — CalculateAlleleFrequency","text":"","code":"CalculateAlleleFrequency(reference_reads, alternative_reads, pseudo_count = 0)"},{"path":"https://costalab.github.io/sigurd/reference/CalculateAlleleFrequency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculating the Minor Allele Frequency. — CalculateAlleleFrequency","text":"reference_reads Reference reads matrix. alternative_reads List matrices alternative reads. pseudo_count = pseudo count want add reference_reads matrix. Default = 0","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateAltReads.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateAltReads — CalculateAltReads","title":"CalculateAltReads — CalculateAltReads","text":"calculate number reads covering variant using forward reverse reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateAltReads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateAltReads — CalculateAltReads","text":"","code":"CalculateAltReads(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateAltReads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateAltReads — CalculateAltReads","text":"SE SummarizedExperiment object. chromosome_prefix List matrices alternative reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateConsensus.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateConsensus — CalculateConsensus","title":"CalculateConsensus — CalculateConsensus","text":"calculate consensus information MAEGATK results. set cells alternative reads 2 (Alternative). set cells reference reads 1 (Reference). set cells mixture alternative reference reads 3 (). set cells reads 0 (NoCall). Please note. Cells can reads reference specific variant reads alternative. cell can still reads alternative alleles. cell still considered 0 (NoCall) variant. example: cell position 3: 0 reads, 53 T reads, 63 C reads, 148 T reads. variant chrM_3_T_A, cell 53 reference reads, also reads variants position. make sure confusion, cell set NoCall.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateConsensus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateConsensus — CalculateConsensus","text":"","code":"CalculateConsensus(SE, chromosome_prefix = \"chrM\", verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/reference/CalculateConsensus.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateConsensus — CalculateConsensus","text":"SE SummarizedExperiment object. chromosome_prefix chromosome name used prefix. verbose function verbose? Default = FALSE","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateCorrelationPValue.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlating the SNVs — CalculateCorrelationPValue","title":"Correlating the SNVs — CalculateCorrelationPValue","text":"perform correlation SNVs calculate P values.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateCorrelationPValue.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlating the SNVs — CalculateCorrelationPValue","text":"","code":"CalculateCorrelationPValue(   variant_values,   other_mutation,   all_variants_list,   min_intersecting_cells = 5 )"},{"path":"https://costalab.github.io/sigurd/reference/CalculateCorrelationPValue.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlating the SNVs — CalculateCorrelationPValue","text":"variant_values fraction values analysing. vector. other_mutation variants . vector variant names. all_variants_list List fraction values variants want compare variant . min_intersecting_cells Minimum number intersecting cells. Correlations less performed.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateCoverage — CalculateCoverage","title":"CalculateCoverage — CalculateCoverage","text":"calculate coverage information per variant MAEGATK results.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateCoverage — CalculateCoverage","text":"","code":"CalculateCoverage(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateCoverage — CalculateCoverage","text":"SE SummarizedExperiment object. chromosome_prefix List matrices alternative reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateFisherTestPValue — CalculateFisherTestPValue","title":"CalculateFisherTestPValue — CalculateFisherTestPValue","text":"perform Fisher Test SNVs calculate P values.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateFisherTestPValue — CalculateFisherTestPValue","text":"","code":"CalculateFisherTestPValue(   variant_values,   other_mutation,   all_variants_list,   min_intersecting_cells = 5 )"},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateFisherTestPValue — CalculateFisherTestPValue","text":"variant_values fraction values analysing. vector. other_mutation variants . vector variant names. all_variants_list List fraction values variants want compare variant . min_intersecting_cells Minimum number intersecting cells. Correlations less performed.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue2.html","id":null,"dir":"Reference","previous_headings":"","what":"We perform the Fisher test of SNVs and calculate the P values. — CalculateFisherTestPValue2","title":"We perform the Fisher test of SNVs and calculate the P values. — CalculateFisherTestPValue2","text":"perform Fisher test SNVs calculate P values.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"We perform the Fisher test of SNVs and calculate the P values. — CalculateFisherTestPValue2","text":"","code":"CalculateFisherTestPValue2(   variant_values,   other_mutation,   all_variants_list,   min_intersecting_cells = 5 )"},{"path":"https://costalab.github.io/sigurd/reference/CalculateFisherTestPValue2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"We perform the Fisher test of SNVs and calculate the P values. — CalculateFisherTestPValue2","text":"variant_values fraction values analysing. vector. other_mutation variants . vector variant names. all_variants_list List fraction values variants want compare variant . min_intersecting_cells Minimum number intersecting cells. Correlations less performed.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateQuality.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateQuality — CalculateQuality","title":"CalculateQuality — CalculateQuality","text":"calculate quality per variant.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateQuality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateQuality — CalculateQuality","text":"","code":"CalculateQuality(SE, variants, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateQuality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateQuality — CalculateQuality","text":"SE SummarizedExperiment object. variants variants want get quality . chromosome_prefix List matrices alternative reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateRefReads.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateRefReads — CalculateRefReads","title":"CalculateRefReads — CalculateRefReads","text":"calculate number reference reads covering variant using forward reverse reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateRefReads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateRefReads — CalculateRefReads","text":"","code":"CalculateRefReads(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateRefReads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateRefReads — CalculateRefReads","text":"SE SummarizedExperiment object. chromosome_prefix List matrices reference reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateStrandCorrelation.html","id":null,"dir":"Reference","previous_headings":"","what":"CalculateStrandCorrelation — CalculateStrandCorrelation","title":"CalculateStrandCorrelation — CalculateStrandCorrelation","text":"calculate correlation amount forward reverse reads per variant.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CalculateStrandCorrelation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CalculateStrandCorrelation — CalculateStrandCorrelation","text":"","code":"CalculateStrandCorrelation(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/CalculateStrandCorrelation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CalculateStrandCorrelation — CalculateStrandCorrelation","text":"SE SummarizedExperiment object. chromosome_prefix List matrices alternative reads.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CallSupport.html","id":null,"dir":"Reference","previous_headings":"","what":"CallSupport — CallSupport","title":"CallSupport — CallSupport","text":"Check cell supported set variants.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CallSupport.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CallSupport — CallSupport","text":"","code":"CallSupport(   SE,   VOI_group1,   VOI_group2,   group1_name = \"group1\",   group2_name = \"group2\",   min_mutated_reads = 3,   min_reads = 30,   group_factor = NULL,   verbose = TRUE,   return_nonsupport = FALSE )"},{"path":"https://costalab.github.io/sigurd/reference/CallSupport.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CallSupport — CallSupport","text":"SE SummarizedExperiment object. VOI_group1 variants supporting first group. VOI_group2 variants supporting second group. group1_name name used first group. group2_name name used second group. min_mutated_reads minimum number mutated reads cell supporting group. min_reads Minimum number reads per cell classification. group_factor much higher mean allele frequency group 1 compared group 2 vice versa? Can vector length 2. verbose function verbose? Default = TRUE return_nonsupport nonsupporting cells return ? Default FALSE. group_of_interest column data divides cells.","code":""},{"path":"https://costalab.github.io/sigurd/reference/ClonalDefinition.html","id":null,"dir":"Reference","previous_headings":"","what":"Defining clones. — ClonalDefinition","title":"Defining clones. — ClonalDefinition","text":"function defines clones using combination variants supplied. set variants can paired identity, like sample cell type. clones determined respect group. information provided, clones determined cells present.","code":""},{"path":"https://costalab.github.io/sigurd/reference/ClonalDefinition.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Defining clones. — ClonalDefinition","text":"","code":"ClonalDefinition(   se,   variants_ls,   grouping = NULL,   identities = NULL,   explicit = FALSE,   explicit_not = NULL,   explicit_min_vaf = 0.01,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/ClonalDefinition.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Defining clones. — ClonalDefinition","text":"se SummarizedExperiment object. variants_ls List variants clonal definition grouping meta data    column used split cells groups. Default = NULL identities Vector groups, like samples. explicit want specify variants forming clone? variant_ls needs list variants define clone. One variant per group. explicit_not want specify set variants cell may ? One set per group. explicit_min_vaf Minimum VAF cell considered positive. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/ClonalDiversity.html","id":null,"dir":"Reference","previous_headings":"","what":"Determining the clonal diversity. — ClonalDiversity","title":"Determining the clonal diversity. — ClonalDiversity","text":"function determines clonal diversity. clones defined using function ClonalDefinition. required use clones, column column data object can used.","code":""},{"path":"https://costalab.github.io/sigurd/reference/ClonalDiversity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determining the clonal diversity. — ClonalDiversity","text":"","code":"ClonalDiversity(   se,   grouping = \"Clones\",   cells = NULL,   diversity_measure = \"EffectiveSpecies\",   base = exp(1),   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/ClonalDiversity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determining the clonal diversity. — ClonalDiversity","text":"se SummarizedExperiment object. grouping meta data    column used. cells cells used? NULL uses cells. diversity_measure diversity measure calculated? Can EffectiveSpecies, shannon, simpson, invsimpson base base diversity verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects.html","id":null,"dir":"Reference","previous_headings":"","what":"CombineSEobjects — CombineSEobjects","title":"CombineSEobjects — CombineSEobjects","text":"combine two SummarizedExperiment objects. originally intended add mitochondrial genotyping information somatic genotyping information. function can combine two objects requried two different genotyping results.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CombineSEobjects — CombineSEobjects","text":"","code":"CombineSEobjects(se_1, se_2, suffixes = c(\"_1\", \"_2\"))"},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CombineSEobjects — CombineSEobjects","text":"se_1 SummarizedExperiment object 1. se_2 SummarizedExperiment object 2. suffixes suffixes want add meta data.frame.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects_big.html","id":null,"dir":"Reference","previous_headings":"","what":"CombineSEobjects_big — CombineSEobjects_big","title":"CombineSEobjects_big — CombineSEobjects_big","text":"combine two SummarizedExperiment objects big matrices.","code":""},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CombineSEobjects_big — CombineSEobjects_big","text":"","code":"CombineSEobjects_big(se_somatic, se_MT, suffixes = c(\"_somatic\", \"_MT\"))"},{"path":"https://costalab.github.io/sigurd/reference/CombineSEobjects_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CombineSEobjects_big — CombineSEobjects_big","text":"se_somatic SummarizedExperiment object somatic variants. se_MT SummarizedExperiment object MT variants. suffixes suffixes want add meta data.frame.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Enrichment_FisherTest.html","id":null,"dir":"Reference","previous_headings":"","what":"Enrichment_FisherTest — Enrichment_FisherTest","title":"Enrichment_FisherTest — Enrichment_FisherTest","text":"function performs Fisher test. specified variant ","code":""},{"path":"https://costalab.github.io/sigurd/reference/Enrichment_FisherTest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Enrichment_FisherTest — Enrichment_FisherTest","text":"","code":"Enrichment_FisherTest(   se = NULL,   variant = NULL,   use_nocall = FALSE,   both_as_alt = TRUE,   trait = NULL,   trait_levels = NULL )"},{"path":"https://costalab.github.io/sigurd/reference/Enrichment_FisherTest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Enrichment_FisherTest — Enrichment_FisherTest","text":"se SummarizedExperiment object. variant variant analysed. values variant retrieved consensus assay. use_nocall NoCall values used? non genotyped cells separate group addition Alt Ref. FALSE, NoCalls removed. Default = FALSE both_as_alt consensus value heterozyguous (3 ) treated homozyguous (Alt)? Default = TRUE trait trait variant associated . can column colData object. trait_levels trait levels used comparison? example, Sample 1-3 present 1 2 used comparison use trait_levels = c(\"Sample_1\", \"Sample_2\"). NULL uses levels. Default = NULL","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":null,"dir":"Reference","previous_headings":"","what":"Filtering the loaded genotyping data. — Filtering","title":"Filtering the loaded genotyping data. — Filtering","text":"filter SummarizedExperiment object exclude variants cells.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filtering the loaded genotyping data. — Filtering","text":"","code":"Filtering(   SE,   cells_include = NULL,   cells_exclude = NULL,   fraction_threshold = NULL,   alts_threshold = NULL,   min_cells_per_variant = NULL,   min_variants_per_cell = NULL,   reject_value = \"NoCall\",   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filtering the loaded genotyping data. — Filtering","text":"SE SummarizedExperiment object. cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. fraction_threshold Variants VAF threshold set 0. Numeric. Default = NULL. alts_threshold Variants number alt reads less threshold set 0. Numeric. Default = NULL. min_cells_per_variant many cells variant present included? Numeric. Default = 2. min_variants_per_cell many variants covered cell included? Default = 1. reject_value cells fall threshold (fraction_threshold alts_threshold) treated Reference NoCall? Default = NoCall. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Filtering the loaded genotyping data. — Filtering","text":"one sample time. want remove: cells allow list, cells exclusion list, cells least one variant >1 (Reference), variants alternative transcripts, variants always NoCall, set variants VAF threshold NoCall Reference.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Filtering the loaded genotyping data. — Filtering","text":"","code":"if (FALSE) {   # Removing all variants that are not detected in at least 2 cells.   # Before we remove the variants, we set fraction value of variants below 0.05 to 0.   se_geno <- Filtering(se_geno, min_cells_per_variant = 2, fraction_threshold = 0.05) }"},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":null,"dir":"Reference","previous_headings":"","what":"Filtering the loaded genotyping data using big matrices. — Filtering_big","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"filter SummarizedExperiment object exclude variants cells.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"","code":"Filtering_big(   se,   blacklisted_barcodes_path = NULL,   fraction_threshold = NULL,   path_seurat = NULL,   min_cells_per_variant = 2 )"},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"se SummarizedExperiment object. blacklisted_barcodes_path Barcodes want remove. Path file one column without header. fraction_threshold Variants VAF threshold set 0. Numeric. path_seurat Path Seurat object. Cells present object removed. min_cells_per_variant many cells variant present included? Numeric. Default = 2. min_variants_per_cell many variants covered cell included? Default = 1.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"one sample time. want remove: cells blacklisted, cells Seurat object, cells least one variant >1 (Reference), variants alternative transcripts, variants always NoCall, set variants VAF threshold reference.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Filtering_big.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Filtering the loaded genotyping data using big matrices. — Filtering_big","text":"","code":"if (FALSE) {   # Removing all variants that are not detected in at least 2 cells.   # Before we remove the variants, we set fraction value of variants below 0.05 to 0.   se_geno <- Filtering(se_geno, min_cells_per_variant = 2, fraction_threshold = 0.05) }"},{"path":"https://costalab.github.io/sigurd/reference/GetCellInfoPerVariant.html","id":null,"dir":"Reference","previous_headings":"","what":"We get the variant information per cell. — GetCellInfoPerVariant","title":"We get the variant information per cell. — GetCellInfoPerVariant","text":"get variant information per cell.","code":""},{"path":"https://costalab.github.io/sigurd/reference/GetCellInfoPerVariant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"We get the variant information per cell. — GetCellInfoPerVariant","text":"","code":"GetCellInfoPerVariant(se, voi_ch, verbose = FALSE)"},{"path":"https://costalab.github.io/sigurd/reference/GetCellInfoPerVariant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"We get the variant information per cell. — GetCellInfoPerVariant","text":"se SummarizedExperiment object. voi_ch Variants interest. verbose function verbose? Default = FALSE","code":""},{"path":"https://costalab.github.io/sigurd/reference/GetVariantInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"GetVariantInfo — GetVariantInfo","title":"GetVariantInfo — GetVariantInfo","text":"get genotyping information set variants. function returns matrix values specified assay.","code":""},{"path":"https://costalab.github.io/sigurd/reference/GetVariantInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GetVariantInfo — GetVariantInfo","text":"","code":"GetVariantInfo(SE, information = \"consensus\", variants = NULL, cells = NULL)"},{"path":"https://costalab.github.io/sigurd/reference/GetVariantInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GetVariantInfo — GetVariantInfo","text":"SE SummarizedExperiment object. information assay desired information. Default: consensus variants vector variants. cells vector cell IDs. default cells returned. Default: NULL","code":""},{"path":"https://costalab.github.io/sigurd/reference/HeatmapVoi.html","id":null,"dir":"Reference","previous_headings":"","what":"HeatmapVoi — HeatmapVoi","title":"HeatmapVoi — HeatmapVoi","text":"plot heatmap set Variants Interest using Variant Allele Frequency values SummarizedExperiment object.","code":""},{"path":"https://costalab.github.io/sigurd/reference/HeatmapVoi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HeatmapVoi — HeatmapVoi","text":"","code":"HeatmapVoi(   SE,   voi,   annotation_trait = NULL,   column_title = NULL,   minimum_coverage = 0,   sort_cells = FALSE,   remove_empty_cells = FALSE,   minimum_allele_freq = 0,   cluster_variants = FALSE,   cluster_variants_distance = \"euclidean\",   cluster_variants_method = \"complete\" )"},{"path":"https://costalab.github.io/sigurd/reference/HeatmapVoi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"HeatmapVoi — HeatmapVoi","text":"SE SummarizedExperiment object. voi Variants Interest. annotation_trait Cell Annotation bottom heat map. column_title title heat map. Default = NULL minimum_coverage minimum coverage per cell plotted. sort_cells cells sorted ordering cells according largest clones? FALSE uses default complete clustering euclidean distance. remove_empty_cells cells fraction 0 variants removed? Default = FALSE minimum_allele_freq Minimum allele frequency include cell. cluster_variants variants clustered? Default FALSE. cluster_variants_distance distance clustering variants. Default euclidean. cluster_variants_method distance variant clustering. Default complete","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingMAEGATK_typewise.html","id":null,"dir":"Reference","previous_headings":"","what":"LoadingMAEGATK_typewise — LoadingMAEGATK_typewise","title":"LoadingMAEGATK_typewise — LoadingMAEGATK_typewise","text":"load MAEGATK output transform compatible VarTrix output. input file specifically formated csv file necessary information run analysis. Note source column input file needs mgaetk mgatk function. case insensitive. want load single sample without use input file, set following variables. samples_path barcodes_path patient samples_file = NULL","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingMAEGATK_typewise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LoadingMAEGATK_typewise — LoadingMAEGATK_typewise","text":"","code":"LoadingMAEGATK_typewise(   samples_file,   patient,   samples_path = NULL,   patient_column = \"patient\",   type_use = \"scRNAseq_MT\",   chromosome_prefix = \"chrM\",   min_cells = 2,   cells_include = NULL,   cells_exclude = NULL,   barcodes_path = NULL,   cellbarcode_length = 18,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingMAEGATK_typewise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"LoadingMAEGATK_typewise — LoadingMAEGATK_typewise","text":"samples_file Path csv file samples loaded. patient patient want load. samples_path Path input folder. patient_column column contains patient information. Use merge, samples merged. type_use type input. rows specified type loaded. chromosome_prefix prefix want use. Default: \"chrM\" min_cells minimum number cells coverage variant. Variants coverage less amount cells removed. Default = 2 cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. barcodes_path Path barcodes file tsv. Default = NULL cellbarcode_length length cell barcode. length actual barcode plus two suffix (-1). Default = 18 verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingRawMatrix_typewise.html","id":null,"dir":"Reference","previous_headings":"","what":"LoadingRawMatrix_typewise — LoadingRawMatrix_typewise","title":"LoadingRawMatrix_typewise — LoadingRawMatrix_typewise","text":"function load dense matrix genotyping information reformat . matrix column cell barcodes, one reference reads one alternative reads. type design matrix used variant name.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingRawMatrix_typewise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LoadingRawMatrix_typewise — LoadingRawMatrix_typewise","text":"","code":"LoadingRawMatrix_typewise(   samples_file,   patient,   patient_column = \"patient\",   variant_use = NULL,   cells_include = NULL,   cells_exclude = NULL,   matrix_column_separator = \",\",   matrix_header = TRUE,   cellbarcode_index = 1,   ref_index = 2,   alt_index = 3,   cellbarcode_length = 18,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingRawMatrix_typewise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"LoadingRawMatrix_typewise — LoadingRawMatrix_typewise","text":"samples_file Path csv file samples loaded. patient patient want load. patient_column column contains patient information. variant_use variant respective matrices. cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. cellbarcode_length length cell barcode. length actual barcode plus two suffix (-1). Default = 18 verbose function verbose? Default = TRUE samples_path Path input folder. Must include barcodes file.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVCF_typewise.html","id":null,"dir":"Reference","previous_headings":"","what":"LoadingVCF_typewise — LoadingVCF_typewise","title":"LoadingVCF_typewise — LoadingVCF_typewise","text":"load cellwise pileup result VCF file. want load single sample without use input file, set following variables. samples_path patient samples_file = NULL Note source column input file needs vcf function. case insensitive. happened reads N allele aligned. can cause problems since variants typically variants lists. can remove variants setting remove_N_alternative TRUE (default). Set option FALSE, really want retain variants.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVCF_typewise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LoadingVCF_typewise — LoadingVCF_typewise","text":"","code":"LoadingVCF_typewise(   samples_file,   samples_path = NULL,   vcf_path,   patient,   patient_column = \"patient\",   type_use = \"scRNAseq_Somatic\",   min_reads = NULL,   min_cells = 2,   cells_include = NULL,   cells_exclude = NULL,   remove_N_alternative = TRUE,   cellbarcode_length = 18,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVCF_typewise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"LoadingVCF_typewise — LoadingVCF_typewise","text":"samples_file Path csv file samples loaded. samples_path Path input folder. vcf_path Path VCF file variants. patient patient want load. patient_column column contains patient information. Use merge, samples merged. type_use type input. rows specified type loaded. min_reads minimum number reads want. Otherwise treat NoCall. Default = NULL. min_cells minimum number cells variant. Otherwise, remove variant. Default = 2. cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. remove_N_alternative Remove variants N alternative, see Description. Default = TRUE cellbarcode_length length cell barcode. length actual barcode plus two suffix (-1). Default = 18 verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix.html","id":null,"dir":"Reference","previous_headings":"","what":"We load the VarTrix results for one patient and merge all types together. — LoadingVarTrix","title":"We load the VarTrix results for one patient and merge all types together. — LoadingVarTrix","text":"load VarTrix results one patient merge types together.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"We load the VarTrix results for one patient and merge all types together. — LoadingVarTrix","text":"","code":"LoadingVarTrix(samples_path, vcf_path, vcf_path_MT, patient)"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"We load the VarTrix results for one patient and merge all types together. — LoadingVarTrix","text":"samples_path Path csv file samples loaded. vcf_path Path VCF file somatic variants. vcf_path_MT Path VCF file MT variants. patient Patient loaded.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":null,"dir":"Reference","previous_headings":"","what":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"function loads VarTrix results outputs list two SummarizedExperiments objects, one somatic variants accompanying mitochondrial variants.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"","code":"LoadingVarTrix(samples_file, vcf_path, vcf_path_MT, patient)"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"samples_file Path input file. One sample per row. contain following columns:patient: patient sample. patient can multiple samples (treated/untreated). samples merged per patient.sample: ID sample.resource: VarTrix MAEGATK input? Must either VarTrix MAEGATK.type: type data? Must one following: scRNAseq_Somatic, scRNAseq_MT, Amplicon_Somatic, Amplicon_MT.input_folder: Path folder, VarTrix output stored.cells: Path barcodes file CellRanger output. vcf_path Path VCF file contains somatic variants interested . vcf_path_MT Path VCF file contains MT variants interested . patient patient want load.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"function loads VarTrix one patients input file. patient multiple samples, samples merged. two types input data, single cell RNA sequencing amplicon data. scRNAseq data result something like 10X assay, amplicon data focuses specific part genome. output CellRanger pipeline. Amplicon data much higher coverage specific area therefore much better areas. scRNAseq data overwritten amplicon data available. output list two SummarizedExperiment objects. object contains two assays:consensus_somatic: consensus information per somatic variant cell.consensus_MT: consensus information per MT variant cell.fraction_somatic: variant allele frequency per somatic variant cell.fraction_MT: variant allele frequency per MT variant cell. consensus information encoded following way:0: Call, reads covering position.1: Reference, reference reads cover position.2: Alternative, mutated reads cover position.3: , alt ref reads cover position.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_ori.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Loading VarTrix results for the down stream analysis. — LoadingVarTrix","text":"return list two objects. SE_Somatic somatic variants results. SE_MT MT variants results.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise.html","id":null,"dir":"Reference","previous_headings":"","what":"LoadingVarTrix_typewise — LoadingVarTrix_typewise","title":"LoadingVarTrix_typewise — LoadingVarTrix_typewise","text":"load different types results (scRNAseq/amplicon MT/amplicon), might need extreme amounts memory. solve issue, load type separately. following function (AmpliconSupplementing), can add amplicon information scRNAseq information. input file specifically formatted csv file necessary information run analysis. Note source column input file needs vartrix function. hard coded case insensitive.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LoadingVarTrix_typewise — LoadingVarTrix_typewise","text":"","code":"LoadingVarTrix_typewise(   samples_file,   samples_path = NULL,   barcodes_path = NULL,   snp_path = NULL,   vcf_path,   patient,   patient_column = \"patient\",   type_use = \"scRNAseq_Somatic\",   min_reads = NULL,   min_cells = 2,   cells_include = NULL,   cells_exclude = NULL,   cellbarcode_length = 18,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"LoadingVarTrix_typewise — LoadingVarTrix_typewise","text":"samples_file Path csv file samples loaded. samples_path Path input folder. Must include barcodes file. barcodes_path path cell barcodes tsv. Default = NULL snp_path Path SNP file used VarTrix (SNV.loci.txt). vcf_path Path VCF file variants. patient patient want load. patient_column column contains patient information. Use merge, samples merged. type_use type input. rows specified type loaded. min_reads minimum number reads want. Otherwise treat NoCall. Default = NULL. min_cells minimum number cells variant. Otherwise, remove variant. Default = 2. cells_include vector cell barcodes. cells retained. cells_exclude vector cell barcodes. cells removed output. cellbarcode_length length cell barcode. length actual barcode plus two suffix (-1). Default = 18 verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise_big.html","id":null,"dir":"Reference","previous_headings":"","what":"Loading VarTrix results using big.matrix — LoadingVarTrix_typewise_big","title":"Loading VarTrix results using big.matrix — LoadingVarTrix_typewise_big","text":"load different types results (scRNAseq/amplicon MT/amplicon), might need extreme amounts memory. solve issue, load type separately. following function (AmpliconSupplementing), can add amplicon information scRNAseq information.","code":""},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Loading VarTrix results using big.matrix — LoadingVarTrix_typewise_big","text":"","code":"LoadingVarTrix_typewise_big(   samples_file,   samples_path = NULL,   barcodes_path = NULL,   snp_path = NULL,   vcf_path,   patient,   sample = NULL,   type_use = \"scRNAseq_Somatic\",   min_reads = 3,   min_cells = 2 )"},{"path":"https://costalab.github.io/sigurd/reference/LoadingVarTrix_typewise_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Loading VarTrix results using big.matrix — LoadingVarTrix_typewise_big","text":"samples_file Path csv file samples loaded. samples_path Path input folder. barcodes_path Path barcodes file. vcf_path Path VCF file variants. patient patient want load. type_use type input. one : scRNAseq_Somatic, Amplicon_Somatic, scRNAseq_MT, Amplicon_MT. min_reads minimum number reads want. Otherwise treat NoCall. yet implemented. min_cells minimum number cells variant. Otherwise, remove variant.","code":""},{"path":"https://costalab.github.io/sigurd/reference/Merging_SE_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Merging list of SummarizedExperiment objects. — Merging_SE_list","title":"Merging list of SummarizedExperiment objects. — Merging_SE_list","text":"function wrapper .(\"cbind\", se).","code":""},{"path":"https://costalab.github.io/sigurd/reference/Merging_SE_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merging list of SummarizedExperiment objects. — Merging_SE_list","text":"","code":"Merging_SE_list(se)"},{"path":"https://costalab.github.io/sigurd/reference/Merging_SE_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merging list of SummarizedExperiment objects. — Merging_SE_list","text":"se SummarizedExperiment object","code":""},{"path":"https://costalab.github.io/sigurd/reference/RowWiseSplit.html","id":null,"dir":"Reference","previous_headings":"","what":"RowWiseSplit — RowWiseSplit","title":"RowWiseSplit — RowWiseSplit","text":"Performing correlation Fisher test association SummarizedExperiment object requires extreme amounts memory. reduce amount memory necessary, instead get individual rows consensus assay. can remove NoCalls (reads) individual vectors, reducing amount memory needed.","code":""},{"path":"https://costalab.github.io/sigurd/reference/RowWiseSplit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RowWiseSplit — RowWiseSplit","text":"","code":"RowWiseSplit(se, n_cores = 1, minimum_reads, remove_nocalls = TRUE)"},{"path":"https://costalab.github.io/sigurd/reference/RowWiseSplit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RowWiseSplit — RowWiseSplit","text":"se SummarizedExperiment object. n_cores Number cores use. remove_nocalls want remove NoCall cells?","code":""},{"path":"https://costalab.github.io/sigurd/reference/SeparatingMatrixToList.html","id":null,"dir":"Reference","previous_headings":"","what":"SeparatingMatrixToList — SeparatingMatrixToList","title":"SeparatingMatrixToList — SeparatingMatrixToList","text":"separate matrix variant information list. variant entry list. NoCalls (cells reads covering variant) can removed. function gets called RowWiseSplit return.","code":""},{"path":"https://costalab.github.io/sigurd/reference/SeparatingMatrixToList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SeparatingMatrixToList — SeparatingMatrixToList","text":"","code":"SeparatingMatrixToList(row_use, total_matrix, remove_nocalls = TRUE)"},{"path":"https://costalab.github.io/sigurd/reference/SeparatingMatrixToList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SeparatingMatrixToList — SeparatingMatrixToList","text":"row_use row separate. total_matrix matrix split. remove_nocalls want remove NoCall cells?","code":""},{"path":"https://costalab.github.io/sigurd/reference/SetVariantInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"SetVariantInfo — SetVariantInfo","title":"SetVariantInfo — SetVariantInfo","text":"add genotyping information set variants Seurat object. function returns Seurat object values specified assay added meta data.","code":""},{"path":"https://costalab.github.io/sigurd/reference/SetVariantInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SetVariantInfo — SetVariantInfo","text":"","code":"SetVariantInfo(   SE,   seurat_object,   information = \"consensus\",   variants = NULL,   consensus_character = TRUE,   consensus_group = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/SetVariantInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SetVariantInfo — SetVariantInfo","text":"SE SummarizedExperiment object. seurat_object Seurat object. information assay desired information. Default: consensus variants vector variants. consensus_character consensus information save character value? consensus_group consensus groups Alt merged? effect information consensus.","code":""},{"path":"https://costalab.github.io/sigurd/reference/UMIQC.html","id":null,"dir":"Reference","previous_headings":"","what":"UMIQC — UMIQC","title":"UMIQC — UMIQC","text":"load molecule_info.h5 file CellRanger plot molecules rank. molecule defined combination UMI CB. molecules ranked number replicates.","code":""},{"path":"https://costalab.github.io/sigurd/reference/UMIQC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UMIQC — UMIQC","text":"","code":"UMIQC(   central_input_file = NULL,   molecule_info_path = NULL,   subset_by_cbs = TRUE,   cellbarcodes_path = NULL,   umi_length = 12,   min_reads = 100,   sep = \",\",   samples_column = \"sample\",   molecule_info_column = \"molecule_info\",   cellbarcode_column = \"cells\",   add_10x_suffix = \"-1\" )"},{"path":"https://costalab.github.io/sigurd/reference/UMIQC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UMIQC — UMIQC","text":"central_input_file Path csv file samples loaded. molecule_info_path Path single molecule_info file. subset_by_cbs list cell barcodes molecule_info.h5 file subset list approved cell barcodes? Default: TRUE cellbarcodes_path Path cell barcodes file. used central input file used. umi_length length UMI. Default = 12 min_reads minimum number reads per molecule. sep separator used samples_file. Default: \",\" samples_column column samples samples_file. Default: \"sample\" molecule_info_column column paths molecule_info files samples_file. Default: \"molecule_info\" cellbarcode_column column paths cell barcodes files central input file. Default: \"cells\" add_10x_suffix suffix added cell barcodes? Default 10X standard: \"-1\"","code":""},{"path":"https://costalab.github.io/sigurd/reference/UMI_seq.html","id":null,"dir":"Reference","previous_headings":"","what":"UMI_seq — UMI_seq","title":"UMI_seq — UMI_seq","text":"function converts numeric UMI representation found 10X molecule_info.h5 file character string.","code":""},{"path":"https://costalab.github.io/sigurd/reference/UMI_seq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UMI_seq — UMI_seq","text":"","code":"UMI_seq(number, umi_length = 12)"},{"path":"https://costalab.github.io/sigurd/reference/UMI_seq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UMI_seq — UMI_seq","text":"number numeric expression UMI. umi_length length UMI. Default = 12","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantBurden — VariantBurden","title":"VariantBurden — VariantBurden","text":"Calculate variant burden per cell. simply sum MAF values per cell.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantBurden — VariantBurden","text":"","code":"VariantBurden(se)"},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantBurden — VariantBurden","text":"se SummarizedExperiment object","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden_big.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the variant burden per cell using big matrices. — VariantBurden_big","title":"Calculate the variant burden per cell using big matrices. — VariantBurden_big","text":"Calculate variant burden per cell using big matrices.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden_big.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the variant burden per cell using big matrices. — VariantBurden_big","text":"","code":"VariantBurden_big(se)"},{"path":"https://costalab.github.io/sigurd/reference/VariantBurden_big.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the variant burden per cell using big matrices. — VariantBurden_big","text":"se SummarizedExperiment object","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantCloneSizeThresholding.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantCloneSizeThresholding — VariantCloneSizeThresholding","title":"VariantCloneSizeThresholding — VariantCloneSizeThresholding","text":"get variants interest using clone size thresholding. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantCloneSizeThresholding.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantCloneSizeThresholding — VariantCloneSizeThresholding","text":"","code":"VariantCloneSizeThresholding(   SE,   min_coverage = 2,   fraction_negative_cells = 0.9,   min_clone_size = 10,   vaf_threshold = 0.5,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantCloneSizeThresholding.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantCloneSizeThresholding — VariantCloneSizeThresholding","text":"SE SummarizedExperiment object. min_coverage Minimum coverage variant needs . fraction_negative_cells fraction negative cells needed. min_clone_size minimum number cells. vaf_threshold Variant Allele Threshold. Cells threshold considered mutated. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantCorrelationHeatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantCorrelationHeatmap — VariantCorrelationHeatmap","title":"VariantCorrelationHeatmap — VariantCorrelationHeatmap","text":"generate heatmap showing correlation somatic variants MT variants. Packages want remove. see used. ggplot2 parallel rcompanion tidyr","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantCorrelationHeatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantCorrelationHeatmap — VariantCorrelationHeatmap","text":"","code":"VariantCorrelationHeatmap(   correlation_results,   output_path = NULL,   patient,   min_alt_cells = 5,   min_correlation = 0.5,   width_use = 2000,   height_use = 2000,   padding_use = c(165, 165, 2, 2),   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantCorrelationHeatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantCorrelationHeatmap — VariantCorrelationHeatmap","text":"correlation_results Data.frame correlation results. output_path Path output folder. patient patient heatmap. min_alt_cells Minimum number mutated cells needed, otherwise correlation plotted. min_correlation Minimum correlation needed. width_use Width heatmap px. height_use Height heatmap px. padding_use Space around heatmap mm. low, variant names might cut . verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantFisherTestHeatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantFisherTestHeatmap — VariantFisherTestHeatmap","title":"VariantFisherTestHeatmap — VariantFisherTestHeatmap","text":"generate heatmap showing Fisher test somatic variants MT variants. Packages want remove.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantFisherTestHeatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantFisherTestHeatmap — VariantFisherTestHeatmap","text":"","code":"VariantFisherTestHeatmap(   fisher_results,   patient,   min_alt_cells = 5,   min_oddsratio = 1,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantFisherTestHeatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantFisherTestHeatmap — VariantFisherTestHeatmap","text":"fisher_results Data.frame correlation results. patient patient heatmap. min_alt_cells Minimum number mutated cells needed, otherwise association plotted. min_oddsratio Minimum correlation needed. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantQuantileThresholding — VariantQuantileThresholding","title":"VariantQuantileThresholding — VariantQuantileThresholding","text":"get variants interest using quantile thresholding. use top_cells top_VAF, supply one quantil value (quantiles = 0.9, thresholds = 0). function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantQuantileThresholding — VariantQuantileThresholding","text":"","code":"VariantQuantileThresholding(   SE,   min_coverage = 2,   quantiles = c(0.1, 0.9),   thresholds = c(0.1, 0.9),   top_cells = NULL,   top_VAF = NULL,   min_quality = NULL,   mean_allele_frequency = 0,   group_of_interest = NULL,   group1 = NULL,   group2 = NULL,   group_factor = NULL,   remove_nocall = TRUE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantQuantileThresholding — VariantQuantileThresholding","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. top_cells number cells least top_VAF percent variant. top_VAF VAF top cells. min_quality minimum quality want Variants Interest. Can ignored setting NULL. mean_allele_frequency minimum mean allele frequency. Default = 0 group_of_interest column data divides cells. group1 first group interest. set, quantiles calculated group. group2 second group interest. group_factor much higher mean allele frequency group 1 compared group 2? remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding_Combined.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined","title":"VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined","text":"get variants interest using quantile thresholding. function combines functions VariantSelection_Quantile, VariantSelection_Group VariantSelection_TopCells. use top_cells top_VAF, supply one quantil value (quantiles = 0.9, thresholds = 0). function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding_Combined.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined","text":"","code":"VariantQuantileThresholding_Combined(   SE,   min_coverage = 2,   quantiles = c(0.1, 0.9),   thresholds = c(0.1, 0.9),   top_cells = NULL,   top_VAF = NULL,   min_quality = NULL,   mean_allele_frequency = 0,   group_of_interest = NULL,   group1 = NULL,   group2 = NULL,   group_factor = NULL,   remove_nocall = TRUE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantQuantileThresholding_Combined.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantQuantileThresholding_Combined — VariantQuantileThresholding_Combined","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. top_cells number cells least top_VAF percent variant. top_VAF VAF top cells. min_quality minimum quality want Variants Interest. Can ignored setting NULL. mean_allele_frequency minimum mean allele frequency. Default = 0 group_of_interest column data divides cells. group1 first group interest. set, quantiles calculated group. group2 second group interest. group_factor much higher mean allele frequency group 1 compared group 2? remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Group.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantSelection_Group — VariantSelection_Group","title":"VariantSelection_Group — VariantSelection_Group","text":"get variants interest selecting variants high VAF difference two groups. function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Group.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantSelection_Group — VariantSelection_Group","text":"","code":"VariantSelection_Group(   SE,   min_coverage = 2,   quantiles = c(0.1, 0.9),   thresholds = c(0.1, 0.9),   min_quality = NULL,   mean_allele_frequency = 0,   group_of_interest = NULL,   group1 = NULL,   group2 = NULL,   group_factor = 5,   remove_nocall = TRUE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Group.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantSelection_Group — VariantSelection_Group","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. min_quality minimum quality want Variants Interest. Can ignored setting NULL. mean_allele_frequency minimum mean allele frequency. Default = 0 group_of_interest column data divides cells. group1 first group interest. set, quantiles calculated group. group2 second group interest. group_factor much higher mean allele frequency group 1 compared group 2? remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantSelection_Quantile — VariantSelection_Quantile","title":"VariantSelection_Quantile — VariantSelection_Quantile","text":"get variants interest using quantile thresholding. function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantSelection_Quantile — VariantSelection_Quantile","text":"","code":"VariantSelection_Quantile(   SE,   min_coverage = 2,   quantiles = c(0.1, 0.9),   thresholds = c(0.1, 0.9),   min_quality = NULL,   mean_allele_frequency = 0,   remove_nocall = FALSE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_Quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantSelection_Quantile — VariantSelection_Quantile","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. min_quality minimum quality want Variants Interest. Can ignored setting NULL. mean_allele_frequency minimum mean allele frequency. Default = 0 remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_TopCells.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantSelection_TopCells — VariantSelection_TopCells","title":"VariantSelection_TopCells — VariantSelection_TopCells","text":"get variants interest selecting small number cells high VAF variant. function adapted Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_TopCells.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantSelection_TopCells — VariantSelection_TopCells","text":"","code":"VariantSelection_TopCells(   SE,   min_coverage = 2,   quantiles = 0.9,   thresholds = 0,   top_cells = 10,   top_VAF = 0.5,   min_quality = NULL,   remove_nocall = TRUE,   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantSelection_TopCells.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantSelection_TopCells — VariantSelection_TopCells","text":"SE SummarizedExperiment object. min_coverage Minimum coverage needed. quantiles lower upper quantile want use. thresholds VAF thresholds want use quantiles. min_quality minimum quality want Variants Interest. Can ignored setting NULL. remove_nocall NoCall cells (consensus = 0) disregarded analysis? verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseCorrelation.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantWiseCorrelation — VariantWiseCorrelation","title":"VariantWiseCorrelation — VariantWiseCorrelation","text":"correlate variants using Pearson correlation. function calls CalculateCorrelationPValue perform actual correlation.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseCorrelation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantWiseCorrelation — VariantWiseCorrelation","text":"","code":"VariantWiseCorrelation(   variants_list,   n_cores = 1,   p_value_adjustment = \"fdr\",   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseCorrelation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantWiseCorrelation — VariantWiseCorrelation","text":"variants_list List fraction values. n_cores Number cores want use. Numeric. p_value_adjustment Method P value adjustment. See p.adjust details. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseFisherTest.html","id":null,"dir":"Reference","previous_headings":"","what":"VariantWiseFisherTest — VariantWiseFisherTest","title":"VariantWiseFisherTest — VariantWiseFisherTest","text":"perform Fisher test determine variants associated. function calls CalculateFisherTestPValue perform actual testing.","code":""},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseFisherTest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VariantWiseFisherTest — VariantWiseFisherTest","text":"","code":"VariantWiseFisherTest(   variants_list,   n_cores = 1,   p_value_adjustment = \"fdr\",   verbose = TRUE )"},{"path":"https://costalab.github.io/sigurd/reference/VariantWiseFisherTest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VariantWiseFisherTest — VariantWiseFisherTest","text":"variants_list List fraction values. n_cores Number cores want use. Numeric. p_value_adjustment Method P value adjustment. See p.adjust details. verbose function verbose? Default = TRUE","code":""},{"path":"https://costalab.github.io/sigurd/reference/char_to_numeric.html","id":null,"dir":"Reference","previous_headings":"","what":"char_to_numeric — char_to_numeric","title":"char_to_numeric — char_to_numeric","text":"function convert heterozygous/homozygous information VCF consensus information VarTrix. used LoadingVCF_typewise.R.","code":""},{"path":"https://costalab.github.io/sigurd/reference/char_to_numeric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"char_to_numeric — char_to_numeric","text":"","code":"char_to_numeric(char_value)"},{"path":"https://costalab.github.io/sigurd/reference/char_to_numeric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"char_to_numeric — char_to_numeric","text":"char_value genotype encoding want convert?","code":""},{"path":"https://costalab.github.io/sigurd/reference/combine_NAMES.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_NAMES — combine_NAMES","title":"combine_NAMES — combine_NAMES","text":"combine two vectors names.","code":""},{"path":"https://costalab.github.io/sigurd/reference/combine_NAMES.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_NAMES — combine_NAMES","text":"","code":"combine_NAMES(x, y)"},{"path":"https://costalab.github.io/sigurd/reference/combine_NAMES.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combine_NAMES — combine_NAMES","text":"x First vector names. y Second vector names.","code":""},{"path":"https://costalab.github.io/sigurd/reference/combine_SparseMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_sparseMatrix — combine_SparseMatrix","title":"combine_sparseMatrix — combine_SparseMatrix","text":"combine two sparse matrices","code":""},{"path":"https://costalab.github.io/sigurd/reference/combine_SparseMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_sparseMatrix — combine_SparseMatrix","text":"","code":"combine_SparseMatrix(matrix_1, matrix_2)"},{"path":"https://costalab.github.io/sigurd/reference/combine_SparseMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combine_sparseMatrix — combine_SparseMatrix","text":"matrix_1 first sparse matrix. matrix_2 second matrix.","code":""},{"path":"https://costalab.github.io/sigurd/reference/computeAFMutMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"computeAFMutMatrix — computeAFMutMatrix","title":"computeAFMutMatrix — computeAFMutMatrix","text":"Calculate allele frequency per variant. Source: https://github.com/petervangalen/MAESTER-2021 can get AF values greater 1, due uninformative reads. See: https://gatk.broadinstitute.org/hc/en-us/articles/360035532252-Allele-Depth-AD--lower--expected https://github.com/caleblareau/mgatk/issues/1 simply set values 1, since actual information case.","code":""},{"path":"https://costalab.github.io/sigurd/reference/computeAFMutMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"computeAFMutMatrix — computeAFMutMatrix","text":"","code":"computeAFMutMatrix(SE, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/computeAFMutMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"computeAFMutMatrix — computeAFMutMatrix","text":"SE SummarizedExperiment object. chromosome_prefix prefix chromosome.","code":""},{"path":"https://costalab.github.io/sigurd/reference/getAltMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"getAltMatrix — getAltMatrix","title":"getAltMatrix — getAltMatrix","text":"get alt values MAEGATK results. Source: https://github.com/petervangalen/MAESTER-2021","code":""},{"path":"https://costalab.github.io/sigurd/reference/getAltMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getAltMatrix — getAltMatrix","text":"","code":"getAltMatrix(SE_object, letter, chromosome_prefix = \"chrM\")"},{"path":"https://costalab.github.io/sigurd/reference/getAltMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getAltMatrix — getAltMatrix","text":"SE_object SummarizedExperiment object. letter base want use. Character. chromosome_prefix chromosome prefix used.","code":""},{"path":"https://costalab.github.io/sigurd/reference/getMutMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"getMutMatrix — getMutMatrix","title":"getMutMatrix — getMutMatrix","text":"function gets allele frequency specific allele. used computeAFMutMatrix. 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+  </url>
+  <url>
+    <loc>https://costalab.github.io/sigurd/reference/getReadMatrix.html</loc>
+  </url>
+  <url>
+    <loc>https://costalab.github.io/sigurd/reference/getRefMatrix.html</loc>
+  </url>
+  <url>
+    <loc>https://costalab.github.io/sigurd/reference/get_consensus.html</loc>
+  </url>
+  <url>
+    <loc>https://costalab.github.io/sigurd/reference/ggsci_pal.html</loc>
+  </url>
+  <url>
+    <loc>https://costalab.github.io/sigurd/reference/index.html</loc>
+  </url>
+  <url>
+    <loc>https://costalab.github.io/sigurd/reference/load_object.html</loc>
+  </url>
+  <url>
+    <loc>https://costalab.github.io/sigurd/reference/save_object.html</loc>
+  </url>
+  <url>
+    <loc>https://costalab.github.io/sigurd/reference/sdiv.html</loc>
+  </url>
 </urlset>
-
diff --git a/tutorials/comparison/10X_CellMixture.Rmd b/tutorials/comparison/10X_CellMixture.Rmd
new file mode 100644
index 0000000..7fbc81b
--- /dev/null
+++ b/tutorials/comparison/10X_CellMixture.Rmd
@@ -0,0 +1,218 @@
+---
+title: "10x CellMixture MAESTER"
+date: "`r Sys.Date()`"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE, dev = "CairoPNG")
+```
+
+## Reproduction of cell mixture results using 10x data
+
+This is a reproduction using the MAESTER script 3.3_TenX_CellLineMix_variants.R
+
+Available here: https://github.com/petervangalen/MAESTER-2021/blob/main/3_Cell_line_mixes_variants/3.3_TenX_CellLineMix_variants.R
+
+## Loading necessary packages.
+
+We load packages necessary for the MAESTER script.
+
+```{r warning = FALSE}
+options(stringsAsFactors = FALSE)
+options(scipen = 999)
+suppressPackageStartupMessages(library(tidyverse))
+suppressPackageStartupMessages(library(SummarizedExperiment))
+suppressPackageStartupMessages(library(Seurat))
+suppressPackageStartupMessages(library(data.table))
+suppressPackageStartupMessages(library(Matrix))
+suppressPackageStartupMessages(library(ComplexHeatmap))
+suppressPackageStartupMessages(library(ggrastr))
+suppressPackageStartupMessages(library(readxl))
+
+# Custom Functions
+cutf <- function(x, f=1, d="/") sapply(strsplit(x, d), function(i) paste(i[f], collapse=d))
+computeAFMutMatrix <- function(SE){
+  cov <- assays(SE)[["coverage"]]+ 0.000001
+  ref_allele <- as.character(rowRanges(SE)$refAllele)
+  getMutMatrix <- function(letter){
+    mat <- (assays(SE)[[paste0(letter, "_counts_fw")]] + assays(SE)[[paste0(letter, "_counts_rev")]]) / cov
+    rownames(mat) <- paste0(as.character(1:dim(mat)[1]), "_", toupper(ref_allele), ">", letter)
+    return(mat[toupper(ref_allele) != letter,])
+  }
+  rbind(getMutMatrix("A"), getMutMatrix("C"), getMutMatrix("G"), getMutMatrix("T"))
+}
+popcol.tib <- read_excel("MAESTER_colors.xlsx")
+mycol.ch <- popcol.tib$hex
+names(mycol.ch) <- popcol.tib$name
+```
+
+## Loading and preparing the data.
+
+```{r warning = FALSE}
+# Import data for 10X 3' v3 Cell Line Mix (available at https://vangalenlab.bwh.harvard.edu/maester-2021/)
+seu <- readRDS("TenX_CellLineMix_Seurat_Keep.rds")
+maegatk_all.rse <- readRDS("TenX_CellLineMix_All_mr3_maegatk.rds")
+
+# Combine information
+common.cells <- intersect(colnames(seu), colnames(maegatk_all.rse))
+
+# Put all objects in the same order
+seu <- seu[,common.cells]
+maegatk.rse <- maegatk_all.rse[,common.cells]
+
+# Prepare allele frequency matrix.
+af.dm <- data.matrix(computeAFMutMatrix(maegatk.rse))*100
+
+# Collect cell information
+cells.tib <- tibble(cell = common.cells,
+                    orig.ident = seu$orig.ident,
+                    CellType_RNA = seu$CellType,
+                    UMAP_1 = seu$UMAP_1,
+                    UMAP_2 = seu$UMAP_2,
+                    Mean_Cov = maegatk.rse$depth)
+
+# Make groups of cell ids
+CellSubsets.ls <- list(unionCells = cells.tib$cell,
+                       K562 = filter(cells.tib, CellType_RNA == "K562")$cell,
+                       BT142 = filter(cells.tib, CellType_RNA == "BT142")$cell)
+
+# Get the mean allele frequency and coverage for every cell subset.
+mean_af.ls <- lapply(CellSubsets.ls, function(x) rowMeans(af.dm[,x]))
+mean_cov.ls <- lapply(CellSubsets.ls, function(x) rowMeans(assays(maegatk.rse)[["coverage"]][,x])[as.numeric(cutf(rownames(af.dm), d = "_"))])
+names(mean_af.ls) <- paste0("mean_af.", names(mean_af.ls))
+names(mean_cov.ls) <- paste0("mean_cov.", names(mean_cov.ls))
+
+# Get the quantiles of the VAFs of each variant in each cell subset
+quantiles <- c("q01" = 0.01, "q10" = 0.1, "q50" = 0.5, "q90" = 0.9, "q99" = 0.99)
+quantiles.ls <- lapply(quantiles, function(x) lapply(CellSubsets.ls, function(y) apply(af.dm[,y], 1, quantile, x) ))
+
+# Get the mean quality for each variant.
+assays.ls <- lapply(maegatk.rse@assays$data, function(x) as.matrix(x))
+qual.num <- sapply(rownames(af.dm), function(x) {
+    #x <- "2141_T>C"
+    pos <- as.numeric( cutf(x, d = "_") )
+    mut <- cutf(x, d = ">", f = 2)
+    # Get the mean quality of reads for this call (only use cells in which the base was sequenced) - forward
+    covered_fw <- assays.ls[[str_c(mut, "_counts_fw")]][pos,] > 0
+    qual_fw <- assays.ls[[str_c(mut, "_qual_fw")]][pos, covered_fw]
+    # Same for reverse
+    covered_rev <- assays.ls[[str_c(mut, "_counts_rev")]][pos,] > 0
+    qual_rev <- assays.ls[[str_c(mut, "_qual_rev")]][pos, covered_rev]
+    qual <- mean(c(qual_fw, qual_rev))
+    return(qual)
+})
+
+# Collect all information in a tibble
+vars.tib <- as_tibble(do.call(cbind, c(mean_af.ls, mean_cov.ls, unlist(quantiles.ls, recursive = F))), rownames = "var")
+vars.tib <- add_column(vars.tib, quality = qual.num, .before = 2)
+
+# Save for fast loading next time
+write_tsv(vars.tib, "TenX_CellLineMix_Variants1.txt")
+```
+
+## Selecting the Variants of Interest
+
+Now, we select the variants of interest.
+
+```{r warning = FALSE, dev = "CairoPNG"}
+# Variants 20-fold coverage, VAF of <10% in the bottom 10% of cells and VAF of >90% in top 10% of cells.
+voi.ch <- vars.tib %>% filter(mean_cov.unionCells > 20,
+                              quality > 30,
+                              q10.unionCells < 10,
+                              q90.unionCells > 90) %>% .$var
+```
+
+## Visualisation
+
+```{r warning = FALSE, dev = "CairoPNG"}
+# Generate matrices with coverage, allele frequency and reference / variant reads
+cov_voi.mat <- assays(maegatk.rse)[["coverage"]][as.numeric(cutf(voi.ch, d = "_")),]
+af_voi.mat <- af.dm[voi.ch,]
+
+# Add coverage and allele frequency info from variants of interest to cells.tib
+for (voi in voi.ch) {
+  cells.tib <- cells.tib %>%
+    left_join(as_tibble(assays(maegatk.rse)[["coverage"]][as.numeric(cutf(voi, d = "_")),], rownames = "cell"), by = "cell") %>%
+    left_join(as_tibble(af.dm[voi,], rownames = "cell"), by = "cell") %>%
+    rename(value.x = str_c("cov_", str_replace(voi, ">", ".")), value.y = str_c("af_", str_replace(voi, ">", ".")))
+}
+
+# Function to sum up the reads supporting either reference or mutant allele for a particulal variant of interest.
+supporting_calls <- function(voi, maegatk) {
+    #voi <- voi.ch[1]
+    #maegatk <- maegatk.rse
+    # From the variant, determine position, reference and mutant allele
+    pos <- as.numeric(cutf(voi, d = "_"))
+    ref <- cutf(voi, d = "_|>|\\.", f = 2)
+    mut <- cutf(voi, d = ">|\\.", f = 2)
+    
+    # Put all the counts for this variant from the maegatk object in a data frame
+    counts.df <- do.call(cbind, lapply(assays(maegatk)[grepl("counts", names(assays(maegatk)))], function(x) x[pos,]))
+    
+    # Add up reads supporting reference or mutated allele
+    support.df <- data.frame(ref = rowSums(counts.df[,grepl(paste0("^", ref), colnames(counts.df))]),
+                             mut = rowSums(counts.df[,grepl(paste0("^", mut), colnames(counts.df))]))
+    
+    support.df
+}
+
+# Calculate number of supporting reads for each variant; then combine
+supporting_calls.ls <- lapply(voi.ch, function(x) supporting_calls(x, maegatk.rse))
+names(supporting_calls.ls) <- voi.ch
+combined_supporting_calls.df <- do.call(cbind, supporting_calls.ls)
+
+# Add up supporting reads: is it a K562 or BT142 cell?
+supporting_calls.tib <- tibble(cell = rownames(combined_supporting_calls.df),
+    K562_supporting_calls = rowSums(combined_supporting_calls.df[,c("709_G>A.mut", "1888_G>A.mut", "6249_G>A.mut", "8697_G>A.mut", "11719_G>A.mut", "15452_C>A.mut", "1420_T>C.mut", "2141_T>C.mut", "4216_T>C.mut", "6524_T>C.mut", "9117_T>C.mut", "11251_A>G.mut", "11764_A>G.mut", "11812_A>G.mut", "15607_A>G.mut", "7990_C>T.ref", "12741_C>T.mut")]),
+    BT142_supporting_calls = rowSums(combined_supporting_calls.df[,c("709_G>A.ref", "1888_G>A.ref", "6249_G>A.ref", "8697_G>A.ref", "11719_G>A.ref", "15452_C>A.ref", "1420_T>C.ref", "2141_T>C.ref", "4216_T>C.ref", "6524_T>C.ref", "9117_T>C.ref", "11251_A>G.ref", "11764_A>G.ref", "11812_A>G.ref", "15607_A>G.ref", "7990_C>T.mut", "12741_C>T.ref")]))
+
+# Combine information
+cells.tib <- left_join(cells.tib, supporting_calls.tib, by = "cell")
+
+# Label cells as K562, BT142, contaminated or NoCoverage based on the number of supporting reads
+cells.tib <- cells.tib %>% mutate(CellType_MT = ifelse(K562_supporting_calls + BT142_supporting_calls < 30, yes = "NoCoverage", no =
+    ifelse(K562_supporting_calls > 3 & K562_supporting_calls > 10*BT142_supporting_calls, yes = "K562", no =
+    ifelse(BT142_supporting_calls > 3 & BT142_supporting_calls > 2*K562_supporting_calls, yes = "BT142", no = "Contaminated")))) %>%
+    mutate(CellType_MT = factor(CellType_MT, levels = c("Contaminated", "BT142", "K562", "NoCoverage")))
+
+cells.ch <- cells.tib %>% filter(CellType_MT %in% c("K562", "BT142")) %>%
+    select(cell, starts_with("cov_")) %>%
+    filter(apply(.[,-1], 1, function(x) all(x > 3))) %>%
+    .$cell
+
+# Create heatmap annotation (RNA-seq clusters)
+ha <- HeatmapAnnotation(CellType_RNA = gsub("BT142_Cycling", "BT142", cells.tib$CellType_RNA[cells.ch]),
+                        col = list(CellType_RNA = c("K562" = "#7BF581", "BT142" = "#8E87F5")))
+
+# Visualize: clustered VAFs
+Heatmap(af_voi.mat[,cells.ch],
+        col=c("#FCFCFC","#FFEDB0","#FFDF5F","#FEC510","#FA8E24","#F14C2B","#DA2828","#BE2222","#A31D1D"),
+        show_row_names = T,
+        show_column_names = F,
+        cluster_columns = T,
+        cluster_rows = F,
+        name = "AF",
+        top_annotation = ha,
+        border = T,
+        width = unit(3.5, "inch"),
+        height = unit(3.5, "inch"),
+        heatmap_legend_param = list(border = "black", at = c(0,25,50,75,100)),
+        use_raster = T)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+```
diff --git a/tutorials/comparison/BoneMarrow.Rmd b/tutorials/comparison/BoneMarrow.Rmd
new file mode 100644
index 0000000..da24d0e
--- /dev/null
+++ b/tutorials/comparison/BoneMarrow.Rmd
@@ -0,0 +1,160 @@
+---
+title: "BPDCN BoneMarrow MAESTER"
+date: "`r Sys.Date()`"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE, dev = "CairoPNG")
+```
+
+## BPDCN BoneMarrow MAESTER Analysis
+
+We reproduce the results from the script 4.2_Variant_Selection.R
+
+Available here: https://github.com/petervangalen/MAESTER-2021/blob/main/4_CH_sample/4.2_Variant_Selection.R
+
+## Loading necessary packages.
+
+We load the data from MAESTER. 
+
+```{r Packages}
+print("Libraries for SIGURD.")
+suppressPackageStartupMessages(library(tidyverse))
+suppressPackageStartupMessages(library(SummarizedExperiment))
+suppressPackageStartupMessages(library(Seurat))
+suppressPackageStartupMessages(library(Matrix))
+suppressPackageStartupMessages(library(readxl))
+suppressPackageStartupMessages(library(ComplexHeatmap))
+suppressPackageStartupMessages(library(circlize))
+suppressPackageStartupMessages(library(magick))
+suppressPackageStartupMessages(library(mclust))
+cutf <- function(x, f=1, d="/") sapply(strsplit(x, d), function(i) paste(i[f], collapse=d))
+computeAFMutMatrix <- function(SE){
+  cov <- assays(SE)[["coverage"]]+ 0.000001
+  ref_allele <- as.character(rowRanges(SE)$refAllele)
+  getMutMatrix <- function(letter){
+    mat <- (assays(SE)[[paste0(letter, "_counts_fw")]] + assays(SE)[[paste0(letter, "_counts_rev")]]) / cov
+    rownames(mat) <- paste0(as.character(1:dim(mat)[1]), "_", toupper(ref_allele), ">", letter)
+    return(mat[toupper(ref_allele) != letter,])
+  }
+  rbind(getMutMatrix("A"), getMutMatrix("C"), getMutMatrix("G"), getMutMatrix("T"))
+}
+var_fc <- function(a, b) {
+  # Distance to homoplasmy
+  x <- min(a, abs(100-a))
+  y <- min(b, abs(100-b))
+  d <- abs(a-b)
+  # Fold difference
+  z <- (min(x,y)+d) / min(x,y)
+  return(z)
+}
+popcol.tib <- read_excel("MAESTER_colors.xlsx")
+mycol.ch <- popcol.tib$hex
+names(mycol.ch) <- popcol.tib$name
+```
+
+## Loading the data using SIGURD.
+
+```{r dev = "CairoPNG"}
+maegatk.rse <- readRDS("BPDCN712_Maegatk_Final.rds")
+seu <- readRDS("BPDCN712_Seurat_with_TCR.rds")
+metadata.tib <- as_tibble(seu@meta.data, rownames = "cell")
+```
+
+## Collect information for each variant
+
+```{r warning = FALSE, dev = "CairoPNG"}
+af.dm <- data.matrix(computeAFMutMatrix(maegatk.rse))*100
+
+assays.ls <- lapply(maegatk.rse@assays$data, function(x) as.matrix(x))
+qual.num <- sapply(rownames(af.dm), function(x) {
+    pos <- as.numeric( cutf(x, d = "_") )
+    mut <- cutf(x, d = ">", f = 2)
+    covered_fw <- assays.ls[[str_c(mut, "_counts_fw")]][pos,] > 0
+    qual_fw <- assays.ls[[str_c(mut, "_qual_fw")]][pos, covered_fw]
+    covered_rev <- assays.ls[[str_c(mut, "_counts_rev")]][pos,] > 0
+    qual_rev <- assays.ls[[str_c(mut, "_qual_rev")]][pos, covered_rev]
+    qual <- mean(c(qual_fw, qual_rev))
+    return(qual)
+})
+vars.tib <- tibble(var = rownames(af.dm),
+                   mean_af = rowMeans(af.dm),
+                   mean_cov = rowMeans(assays(maegatk.rse)[["coverage"]])[as.numeric(cutf(rownames(af.dm), d = "_"))],
+                   quality = qual.num)
+vars.tib <- vars.tib %>%
+  mutate(n0 = apply(af.dm, 1, function(x) sum(x == 0))) %>%
+  mutate(n1 = apply(af.dm, 1, function(x) sum(x > 1))) %>%
+  mutate(n5 = apply(af.dm, 1, function(x) sum(x > 5))) %>%
+  mutate(n10 = apply(af.dm, 1, function(x) sum(x > 10))) %>%
+  mutate(n50 = apply(af.dm, 1, function(x) sum(x > 50)))
+```
+
+## Generate a blocklist
+
+```{r warning = FALSE}
+backgroundvars.tib <- read_tsv("TenX_CellLineMix_Variants1.txt")
+backgroundvars.tib <- backgroundvars.tib %>% select(var, mean_cov.unionCells, mean_af.K562, mean_af.BT142)
+backgroundvars.tib$FoldChange <- apply(backgroundvars.tib, 1, function(x) var_fc(as.numeric(x[3]), as.numeric(x[4])) )
+blocklist.var <- backgroundvars.tib %>% filter(mean_cov.unionCells > 5) %>%
+    filter(between(mean_af.K562, 0.1, 99.9), between(mean_af.BT142, 0.1, 99.9), FoldChange < 5) %>% .$var
+blocklist.var <- c(blocklist.var, backgroundvars.tib[grepl("N", backgroundvars.tib$var),]$var)
+```
+
+## Select VOIs
+
+```{r warning = FALSE}
+conditions.tib <- tibble(min_clone_size = rep(1:25, 4),
+                         min_vaf = rep(c("n1", "n5", "n10", "n50"), each = 25),
+                         vois = NA,
+                         n_vois = NA,
+                         cells = NA,
+                         n_cells = NA,
+                         transitions = NA)
+vois.ls <- vector(mode = "list", length = nrow(conditions.tib))
+cells.ls <- vector(mode = "list", length = nrow(conditions.tib))
+vars_filter.tib <- vars.tib %>% filter(mean_cov > 5, quality >= 30, n0 > 0.9*ncol(af.dm))
+for(x in 1:nrow(conditions.tib)){
+    min_clone_size <- conditions.tib$min_clone_size[x]
+    min_vaf <- conditions.tib$min_vaf[x]
+    voi.ch <- vars_filter.tib$var[vars_filter.tib[[min_vaf]] >= min_clone_size]
+    voi.ch <- setdiff(voi.ch, c("1583_A>G", blocklist.var))
+    af_subset.dm <- af.dm[voi.ch,]
+    positive_cells <- colnames( af_subset.dm[,colSums(af_subset.dm > 1)] )
+    conditions.tib[x,"n_vois"] <- length(voi.ch)
+    conditions.tib[x,"n_cells"] <- length(positive_cells)
+    conditions.tib[x,"transitions"] <- mean( str_count(voi.ch, "G>A|A>G|C>T|T>C") )
+    vois.ls[[x]] <- voi.ch
+    cells.ls[[x]] <- positive_cells
+}
+conditions.tib$vois <- vois.ls
+conditions.tib$cells <- cells.ls
+conditions_subset.tib <- conditions.tib %>% filter(min_clone_size %in% c(5,10), min_vaf %in% c("n10","n50"))
+voi.ch <- conditions_subset.tib$vois[[4]]
+print(voi.ch)
+```
+
+## Visualisation
+
+```{r warning = FALSE, fig.width = 6, dev = "CairoPNG"}
+af_voi.mat <- af.dm[voi.ch, ]
+af_subset.mat <- af_voi.mat[,apply(af_voi.mat, 2, function(x) sum(x > 1) > 0)]
+plot_order.mat <- af_subset.mat
+for (x in rev(voi.ch)) { plot_order.mat <- plot_order.mat[,order(-plot_order.mat[x,])] }
+anno.tib <- tibble(cell = colnames(plot_order.mat)) %>% left_join(metadata.tib, by = "cell") %>% select(CellType)
+ha <- HeatmapAnnotation(df = data.frame(anno.tib), col = list(CellType = mycol.ch))
+Heatmap(plot_order.mat,
+        col = colorRamp2(seq(0, round(max(plot_order.mat)), length.out = 9),
+                         c("#FCFCFC","#FFEDB0","#FFDF5F","#FEC510","#FA8E24","#F14C2B","#DA2828","#BE2222","#A31D1D")),
+        show_row_names = ifelse(nrow(plot_order.mat) < 100, T, F),
+        show_column_names = F,
+        cluster_columns = F,
+        cluster_rows = F,
+        row_names_gp = gpar(fontsize = 10),
+        name = "AF",
+        heatmap_legend_param = list(border = "#000000", grid_height = unit(10, "mm")),
+        top_annotation = ha,
+        border = T,
+        use_raster = T,
+        raster_quality = 5)
+```
diff --git a/tutorials/comparison/SW_CellMixture.Rmd b/tutorials/comparison/SW_CellMixture.Rmd
new file mode 100644
index 0000000..492aef4
--- /dev/null
+++ b/tutorials/comparison/SW_CellMixture.Rmd
@@ -0,0 +1,179 @@
+---
+title: "SW CellMixture MAESTER"
+date: "`r Sys.Date()`"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE, dev = "CairoPNG")
+```
+
+## Reproduction of cell mixture results using Seq-Well data
+
+This is a reproduction using the MAESTER script 3.1_SW_CellLineMix_variants.R.
+
+Available here: https://github.com/petervangalen/MAESTER-2021/blob/main/3_Cell_line_mixes_variants/3.1_SW_CellLineMix_variants.R
+
+## Loading necessary packages.
+
+We load packages necessary for the MAESTER script.
+
+```{r Packages}
+print("Libraries for MAESTER.")
+options(stringsAsFactors = FALSE)
+options(scipen = 999)
+suppressPackageStartupMessages(library(tidyverse))
+suppressPackageStartupMessages(library(SummarizedExperiment))
+suppressPackageStartupMessages(library(Seurat))
+suppressPackageStartupMessages(library(data.table))
+suppressPackageStartupMessages(library(Matrix))
+suppressPackageStartupMessages(library(ComplexHeatmap))
+suppressPackageStartupMessages(library(readxl))
+suppressPackageStartupMessages(library(ggrastr))
+```
+
+## Loading the data using the MAESTER script.
+
+We load the data using the MAESTER script. This requires the use of multiple functions and objects.
+
+```{r warning = FALSE, dev = "CairoPNG"}
+popcol.tib <- read_excel("MAESTER_colors.xlsx")
+mycol.ch <- popcol.tib$hex
+names(mycol.ch) <- popcol.tib$name
+# Custom Functions
+cutf <- function(x, f=1, d="/") sapply(strsplit(x, d), function(i) paste(i[f], collapse=d))
+computeAFMutMatrix <- function(SE){
+  cov <- assays(SE)[["coverage"]]+ 0.000001
+  ref_allele <- as.character(rowRanges(SE)$refAllele)
+  getMutMatrix <- function(letter){
+    mat <- (assays(SE)[[paste0(letter, "_counts_fw")]] + assays(SE)[[paste0(letter, "_counts_rev")]]) / cov
+    rownames(mat) <- paste0(as.character(1:dim(mat)[1]), "_", toupper(ref_allele), ">", letter)
+    return(mat[toupper(ref_allele) != letter,])
+  }
+  rbind(getMutMatrix("A"), getMutMatrix("C"), getMutMatrix("G"), getMutMatrix("T"))
+}
+
+# Loading the scRNAseq data.
+seu <- readRDS("SW_CellLineMix_Seurat_Keep.rds")
+
+# Loading the MAEGATK results.
+maegatk_all.rse <- readRDS("SW_CellLineMix_All_mr3_maegatk.rds")
+
+# Intersecting the cells. We retain only cells that are in both data sets.
+common.cells <- intersect(colnames(seu), colnames(maegatk_all.rse))
+seu <- seu[,common.cells]
+maegatk.rse <- maegatk_all.rse[,common.cells]
+
+# Calculating the allele frequency per cell and possible variant.
+af.dm <- data.matrix(computeAFMutMatrix(maegatk.rse))*100
+
+# Organizing the cellular meta data in a tibble.
+cells.tib <- tibble(cell = common.cells,
+                    orig.ident = seu$orig.ident,
+                    CellType_RNA = seu$CellType,
+                    Mean_Cov = maegatk.rse$depth)
+
+# Separating the cells into distinct subgroups.
+CellSubsets.ls <- list(unionCells = cells.tib$cell,
+                       K562 = filter(cells.tib, CellType_RNA == "K562")$cell,
+                       BT142 = filter(cells.tib, CellType_RNA == "BT142")$cell)
+
+# Calculating the average allele frequency per variant.
+mean_af.ls <- lapply(CellSubsets.ls, function(x) rowMeans(af.dm[,x]))
+names(mean_af.ls) <- paste0("mean.af.", names(mean_af.ls))
+
+# Calculating the average coverage per variant.
+mean_cov.ls <- lapply(CellSubsets.ls, function(x) rowMeans(assays(maegatk.rse)[["coverage"]][,x])[as.numeric(cutf(rownames(af.dm), d = "_"))])
+names(mean_cov.ls) <- paste0("mean.cov.", names(mean_cov.ls))
+
+# Calculating the allele frequency quantile per variant.
+quantiles <- c("q01" = 0.01, "q10" = 0.1, "q50" = 0.5, "q90" = 0.9, "q99" = 0.99)
+quantiles.ls <- lapply(quantiles, function(x) lapply(CellSubsets.ls, function(y) apply(af.dm[,y], 1, quantile, x) ))
+assays.ls <- lapply(maegatk.rse@assays$data, function(x) as.matrix(x))
+qual.num <- sapply(rownames(af.dm), function(x){
+  pos <- as.numeric(cutf(x, d = "_"))
+  mut <- cutf(x, d = ">", f = 2)
+  covered_fw <- assays.ls[[str_c(mut, "_counts_fw")]][pos,] > 0
+  qual_fw <- assays.ls[[str_c(mut, "_qual_fw")]][pos, covered_fw]
+  covered_rev <- assays.ls[[str_c(mut, "_counts_rev")]][pos,] > 0
+  qual_rev <- assays.ls[[str_c(mut, "_qual_rev")]][pos, covered_rev]
+  qual <- mean(c(qual_fw, qual_rev))
+  return(qual)
+})
+
+# Organizing the results in a variant-wise tibble.
+vars.tib <- as_tibble(do.call(cbind, c(mean_af.ls, mean_cov.ls, unlist(quantiles.ls, recursive = F))), rownames = "var")
+vars.tib <- add_column(vars.tib, quality = qual.num, .before = 2)
+```
+
+## Selecting the Variants of Interest
+
+Now, we select the variants of interest.
+
+```{r dev = "CairoPNG"}
+# Identifying variants of interest by subsetting the variant-wise tibble.
+voi.ch <- vars.tib %>% filter(mean.cov.unionCells > 20,
+                              quality > 30,
+                              q10.unionCells < 10,
+                              q90.unionCells > 90) %>% .$var
+print(voi.ch)
+```
+
+## Plotting the mtVOIs as a heatmap
+
+```{r dev = "CairoPNG"}
+# Generate matrices with coverage, allele frequency and reference / variant reads
+cov_voi.mat <- assays(maegatk.rse)[["coverage"]][as.numeric(cutf(voi.ch, d = "_")),]
+af_voi.mat <- af.dm[voi.ch,]
+
+# Add coverage and allele frequency info from variants of interest to cells.tib
+for (voi in voi.ch) {
+  cells.tib <- cells.tib %>%
+    left_join(as_tibble(assays(maegatk.rse)[["coverage"]][as.numeric(cutf(voi, d = "_")),], rownames = "cell"), by = "cell") %>%
+    left_join(as_tibble(af.dm[voi,], rownames = "cell"), by = "cell") %>%
+    rename(value.x = str_c("cov_", str_replace(voi, ">", ".")), value.y = str_c("af_", str_replace(voi, ">", ".")))
+}
+
+# Calculating the support of each cell.
+supporting_calls <- function(voi, maegatk) {
+    # From the variant, determine position, reference and mutant allele
+    pos <- as.numeric(cutf(voi, d = "_"))
+    ref <- cutf(voi, d = "_|>|\\.", f = 2)
+    mut <- cutf(voi, d = ">|\\.", f = 2)
+    # Put all the counts for this variant from the maegatk object in a data frame
+    counts.df <- do.call(cbind, lapply(assays(maegatk)[grepl("counts", names(assays(maegatk)))], function(x) x[pos,]))
+    # Add up reads supporting reference or mutated allele
+    support.df <- data.frame(ref = rowSums(counts.df[,grepl(paste0("^", ref), colnames(counts.df))]),
+                             mut = rowSums(counts.df[,grepl(paste0("^", mut), colnames(counts.df))]))
+    support.df
+}
+supporting_calls.ls <- lapply(voi.ch, function(x) supporting_calls(x, maegatk.rse))
+names(supporting_calls.ls) <- voi.ch
+combined_supporting_calls.df <- do.call(cbind, supporting_calls.ls)
+
+supporting_calls.tib <- tibble(cell = rownames(combined_supporting_calls.df),
+    K562_supporting_calls = rowSums(combined_supporting_calls.df[,c("709_G>A.mut", "1888_G>A.mut", "1420_T>C.mut", "2141_T>C.mut", "9117_T>C.mut", "7990_C>T.ref")]),
+    BT142_supporting_calls = rowSums(combined_supporting_calls.df[,c("709_G>A.ref", "1888_G>A.ref", "1420_T>C.ref", "2141_T>C.ref", "9117_T>C.ref", "7990_C>T.mut")]))
+# Combine information
+cells.tib <- left_join(cells.tib, supporting_calls.tib, by = "cell")
+
+cells.tib <- cells.tib %>% mutate(CellType_MT = ifelse(K562_supporting_calls + BT142_supporting_calls < 30, yes = "NoCoverage", no =
+    ifelse(K562_supporting_calls > 3 & K562_supporting_calls > 10*BT142_supporting_calls, yes = "K562", no =
+    ifelse(BT142_supporting_calls > 3 & BT142_supporting_calls > 10*K562_supporting_calls, yes = "BT142", no = "Contaminated")))) %>%
+    mutate(CellType_MT = factor(CellType_MT, levels = c("Contaminated", "BT142", "K562", "NoCoverage")))
+
+# Selecting cells that have sufficient coverage for all the variants of interest.
+cells.ch <- cells.tib %>% filter(CellType_MT %in% c("K562", "BT142")) %>%
+    select(cell, starts_with("cov_")) %>%
+    filter(apply(.[,-1], 1, function(x) all(x > 3))) %>%
+    .$cell
+
+# Generating the annotation object for the heatmap.
+ha <- HeatmapAnnotation(CellType_RNA = cells.tib$CellType_RNA[cells.ch],
+                        col = list(CellType_RNA = c("K562" = "#7BF581", "BT142" = "#8E87F5")))
+
+# Visualize: clustered VAFs
+Heatmap(af_voi.mat[,cells.ch], name = "VAF", col=c("#FCFCFC","#FFEDB0","#FFDF5F","#FEC510","#FA8E24","#F14C2B","#DA2828","#BE2222","#A31D1D"), show_row_names = TRUE, show_column_names = FALSE, cluster_columns = TRUE, cluster_rows = FALSE, top_annotation = ha, border = TRUE,
+               heatmap_legend_param = list(border = "black", at = c(0,25,50,75,100)), use_raster = TRUE)
+```
+
diff --git a/vignettes/BoneMarrow_SIGURD.Rmd b/vignettes/BoneMarrow_SIGURD.Rmd
index 074730a..321bfc5 100644
--- a/vignettes/BoneMarrow_SIGURD.Rmd
+++ b/vignettes/BoneMarrow_SIGURD.Rmd
@@ -69,7 +69,7 @@ print(voi.ch.sigurd)
 
 ## Visualisation using SIGURD
 
-```{r Vis_SIGURD, fig.width = 6, fig.height = 4, warning = FALSE}
+```{r Vis_SIGURD, fig.width = 6, fig.height = 4, warning = FALSE, dev = "CairoPNG"}
 genotyping <- Filtering(SE = genotyping, cells_include = colnames(scrna))
 colData(genotyping)$CellType <- scrna$CellType
 HeatmapVoi(SE = genotyping, voi = voi.ch.sigurd, annotation_trait = "CellType", sort_cells = TRUE, remove_empty_cells = TRUE, minimum_allele_freq = 0.01)
@@ -79,7 +79,7 @@ HeatmapVoi(SE = genotyping, voi = voi.ch.sigurd, annotation_trait = "CellType",
 
 We check the cell type enrichment for the variant 2593G>A.
 
-```{r warning = FALSE}
+```{r fig.width = 6, fig.height = 4, warning = FALSE, dev = "CairoPNG"}
 result_enrichment <- Enrichment_FisherTest(se = genotyping, variant = "chrM_2593_G_A", use_nocall = FALSE, trait = "CellType")
 ComplexHeatmap::Heatmap(as.matrix(result_enrichment$Heatmap_Values), cluster_rows = FALSE, cluster_columns = FALSE, col= circlize::colorRamp2(c(0, max(result_enrichment$Heatmap_Values, na.rm = TRUE)), c("white", "red")))
 ```
diff --git a/vignettes/BoneMarrow_SIGURD.html b/vignettes/BoneMarrow_SIGURD.html
deleted file mode 100644
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-
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-
-<h1 class="title toc-ignore">Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</h1>
-<h4 class="author">Martin Grasshoff</h4>
-
-
-
-<div id="analysis-of-blastic-plasmacytoid-dendritic-cell-neoplasm-bpdcn" class="section level2">
-<h2>Analysis of Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)</h2>
-<p>Here, we compare the analysis of cells from a patient with BPDCN.</p>
-<p>The original script is available here: <a href="https://github.com/petervangalen/MAESTER-2021/blob/main/4_CH_sample/4.2_Variant_Selection.R" class="uri">https://github.com/petervangalen/MAESTER-2021/blob/main/4_CH_sample/4.2_Variant_Selection.R</a></p>
-<p>In this setup, the cells are all from a single donor and do not have to be separated into categories.</p>
-<p>Then small clones that might characterize the clonal lineages in the sample are selected.</p>
-</div>
-<div id="loading-necessary-packages." class="section level2">
-<h2>Loading necessary packages.</h2>
-<p>We load the data from MAESTER.</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">print</span>(<span class="st">&quot;Libraries for SIGURD.&quot;</span>)</a></code></pre></div>
-<pre><code>## [1] &quot;Libraries for SIGURD.&quot;</code></pre>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">suppressPackageStartupMessages</span>(<span class="kw">library</span>(sigurd))</a>
-<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw">suppressPackageStartupMessages</span>(<span class="kw">library</span>(SummarizedExperiment))</a>
-<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="kw">suppressPackageStartupMessages</span>(<span class="kw">library</span>(ggplot2))</a></code></pre></div>
-</div>
-<div id="loading-the-data-using-sigurd." class="section level2">
-<h2>Loading the data using SIGURD.</h2>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="co"># The design matrix contains information for the genotyping data.</span></a>
-<a class="sourceLine" id="cb4-2" data-line-number="2">genotyping &lt;-<span class="st"> </span><span class="kw">LoadingMAEGATK_typewise</span>(<span class="dt">patient =</span> <span class="st">&quot;BPDCN712&quot;</span>, <span class="dt">samples_file =</span> <span class="st">&quot;/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv&quot;</span>, <span class="dt">type_use =</span> <span class="st">&quot;Amplicon_MT&quot;</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb4-3" data-line-number="3"></a>
-<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># Loading the scRNA-seq data.</span></a>
-<a class="sourceLine" id="cb4-5" data-line-number="5">scrna &lt;-<span class="st"> </span><span class="kw">readRDS</span>(<span class="st">&quot;/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/BPDCN712_Seurat_with_TCR_Renamed.rds&quot;</span>)</a></code></pre></div>
-</div>
-<div id="generating-a-block-list" class="section level2">
-<h2>Generating a block list</h2>
-<p>Variants that are also detected in the cell mixture data is treated as possible false positives. They are used as a blacklist and are removed from the results.</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># Loading the TenX Cell Mixture Genotyping.</span></a>
-<a class="sourceLine" id="cb5-2" data-line-number="2"></a>
-<a class="sourceLine" id="cb5-3" data-line-number="3">genotyping_tenx &lt;-<span class="st"> </span><span class="kw">load_object</span>(<span class="st">&quot;/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/TenX_CellMixture_Genotyping.rds.lz4&quot;</span>)</a>
-<a class="sourceLine" id="cb5-4" data-line-number="4">blocklist &lt;-<span class="st"> </span><span class="kw">AllelFrequencyFoldChange</span>(genotyping_tenx, <span class="dt">group_of_interest =</span> <span class="st">&quot;CellType&quot;</span>, <span class="dt">group1 =</span> <span class="st">&quot;K562&quot;</span>, <span class="dt">group2 =</span> <span class="st">&quot;BT142&quot;</span>, <span class="dt">maximum_foldchange =</span> <span class="dv">5</span>, <span class="dt">minimum_coverage =</span> <span class="dv">5</span>, <span class="dt">minimum_allele_freq =</span> <span class="fl">0.001</span>, <span class="dt">maximum_allele_freq =</span> <span class="fl">0.999</span>)<span class="op">$</span>Variant</a>
-<a class="sourceLine" id="cb5-5" data-line-number="5"></a>
-<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># We add the variant chrM_1583_A_G by hand. It is identified as misleading based on downstream analysis.</span></a>
-<a class="sourceLine" id="cb5-7" data-line-number="7">blocklist &lt;-<span class="st"> </span><span class="kw">c</span>(blocklist, <span class="st">&quot;chrM_1583_A_G&quot;</span>)</a></code></pre></div>
-</div>
-<div id="selecting-the-variants-of-interest" class="section level2">
-<h2>Selecting the Variants of Interest</h2>
-<p>Now, we select the variants of interest from the loaded data.</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">voi.ch.sigurd &lt;-<span class="st"> </span><span class="kw">VariantSelection_TopCells</span>(genotyping, <span class="dt">min_coverage =</span> <span class="dv">5</span>, <span class="dt">quantiles =</span> <span class="fl">0.9</span>, <span class="dt">thresholds =</span> <span class="dv">0</span>, <span class="dt">top_cells =</span> <span class="dv">10</span>, <span class="dt">top_VAF =</span> <span class="fl">0.5</span>, <span class="dt">min_quality =</span> <span class="dv">30</span>, <span class="dt">remove_nocall =</span> <span class="ot">FALSE</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb6-2" data-line-number="2">voi.ch.sigurd &lt;-<span class="st"> </span>voi.ch.sigurd[<span class="op">!</span>voi.ch.sigurd <span class="op">%in%</span><span class="st"> </span>blocklist]</a>
-<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="kw">print</span>(voi.ch.sigurd)</a></code></pre></div>
-<pre><code>##  [1] &quot;chrM_683_G_A&quot;   &quot;chrM_1323_G_A&quot;  &quot;chrM_1415_G_A&quot;  &quot;chrM_2593_G_A&quot; 
-##  [5] &quot;chrM_6205_G_A&quot;  &quot;chrM_6243_G_A&quot;  &quot;chrM_8697_G_A&quot;  &quot;chrM_9753_G_A&quot; 
-##  [9] &quot;chrM_10158_T_A&quot; &quot;chrM_15140_G_A&quot; &quot;chrM_15812_G_A&quot; &quot;chrM_779_T_C&quot;  
-## [13] &quot;chrM_3988_T_C&quot;  &quot;chrM_6185_T_C&quot;  &quot;chrM_6293_T_C&quot;  &quot;chrM_9164_T_C&quot; 
-## [17] &quot;chrM_9321_T_C&quot;  &quot;chrM_11864_T_C&quot; &quot;chrM_15299_T_C&quot; &quot;chrM_1171_A_G&quot; 
-## [21] &quot;chrM_1222_A_G&quot;  &quot;chrM_2241_A_G&quot;  &quot;chrM_2623_A_G&quot;  &quot;chrM_3628_A_G&quot; 
-## [25] &quot;chrM_4104_A_G&quot;  &quot;chrM_6218_A_G&quot;</code></pre>
-</div>
-<div id="visualisation-using-sigurd" class="section level2">
-<h2>Visualisation using SIGURD</h2>
-<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">genotyping &lt;-<span class="st"> </span><span class="kw">Filtering</span>(<span class="dt">SE =</span> genotyping, <span class="dt">cells_include =</span> <span class="kw">colnames</span>(scrna))</a></code></pre></div>
-<pre><code>## [1] &quot;We remove all cells not in the allow list.&quot;
-## [1] &quot;We remove all the variants that are always NoCall.&quot;</code></pre>
-<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw">colData</span>(genotyping)<span class="op">$</span>CellType &lt;-<span class="st"> </span>scrna<span class="op">$</span>CellType</a>
-<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="kw">HeatmapVoi</span>(<span class="dt">SE =</span> genotyping, <span class="dt">voi =</span> voi.ch.sigurd, <span class="dt">annotation_trait =</span> <span class="st">&quot;CellType&quot;</span>, <span class="dt">sort_cells =</span> <span class="ot">TRUE</span>, <span class="dt">remove_empty_cells =</span> <span class="ot">TRUE</span>, <span class="dt">minimum_allele_freq =</span> <span class="fl">0.01</span>)</a></code></pre></div>
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" /><!-- --></p>
-</div>
-<div id="cell-type-enrichment-2593ga" class="section level2">
-<h2>Cell Type Enrichment 2593G&gt;A</h2>
-<p>We check the cell type enrichment for the variant 2593G&gt;A.</p>
-<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">result_enrichment &lt;-<span class="st"> </span><span class="kw">Enrichment_FisherTest</span>(<span class="dt">se =</span> genotyping, <span class="dt">variant =</span> <span class="st">&quot;chrM_2593_G_A&quot;</span>, <span class="dt">use_nocall =</span> <span class="ot">FALSE</span>, <span class="dt">trait =</span> <span class="st">&quot;CellType&quot;</span>)</a></code></pre></div>
-<pre><code>## [1] &quot;We get a count matrix of the chrM_2593_G_A per CellType.&quot;</code></pre>
-<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">ComplexHeatmap<span class="op">::</span><span class="kw">Heatmap</span>(<span class="kw">as.matrix</span>(result_enrichment<span class="op">$</span>Heatmap_Values), <span class="dt">cluster_rows =</span> <span class="ot">FALSE</span>, <span class="dt">cluster_columns =</span> <span class="ot">FALSE</span>, <span class="dt">col=</span> circlize<span class="op">::</span><span class="kw">colorRamp2</span>(<span class="kw">c</span>(<span class="dv">0</span>, <span class="kw">max</span>(result_enrichment<span class="op">$</span>Heatmap_Values, <span class="dt">na.rm =</span> <span class="ot">TRUE</span>)), <span class="kw">c</span>(<span class="st">&quot;white&quot;</span>, <span class="st">&quot;red&quot;</span>)))</a></code></pre></div>
-<p><img 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" /><!-- --></p>
-</div>
-<div id="cell-type-enrichment-6243ga" class="section level2">
-<h2>Cell Type Enrichment 6243G&gt;A</h2>
-<p>We check the cell type enrichment for the variant 6243G&gt;A.</p>
-<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">result_enrichment &lt;-<span class="st"> </span><span class="kw">Enrichment_FisherTest</span>(<span class="dt">se =</span> genotyping, <span class="dt">variant =</span> <span class="st">&quot;chrM_6243_G_A&quot;</span>, <span class="dt">use_nocall =</span> <span class="ot">FALSE</span>, <span class="dt">trait =</span> <span class="st">&quot;CellType&quot;</span>)</a></code></pre></div>
-<pre><code>## [1] &quot;We get a count matrix of the chrM_6243_G_A per CellType.&quot;</code></pre>
-<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1">ComplexHeatmap<span class="op">::</span><span class="kw">Heatmap</span>(<span class="kw">as.matrix</span>(result_enrichment<span class="op">$</span>Heatmap_Values), <span class="dt">cluster_rows =</span> <span class="ot">FALSE</span>, <span class="dt">cluster_columns =</span> <span class="ot">FALSE</span>, <span class="dt">col=</span> circlize<span class="op">::</span><span class="kw">colorRamp2</span>(<span class="kw">c</span>(<span class="dv">0</span>, <span class="kw">max</span>(result_enrichment<span class="op">$</span>Heatmap_Values, <span class="dt">na.rm =</span> <span class="ot">TRUE</span>)), <span class="kw">c</span>(<span class="st">&quot;white&quot;</span>, <span class="st">&quot;red&quot;</span>)))</a></code></pre></div>
-<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAASAAAAEgCAIAAACb4TnXAAAABmJLR0QA/wD/AP+gvaeTAAAgAElEQVR4nO3dZ1gTSxcA4LO7CaH3KuAHgoKA2LCC2LFeBQWkiB0LioqKXdSrqAgCihWvV69dEewFxYoNxI69I6h0kJq2+/0ApIUSNAlJ5n3yA8LuZoA9O7Ozc2YwiqIAQRDBwEVdAASRZCjAEESAUIAhiAChAEMQAUIBhiAChAIMQQSIxvPd69evC7kcCF/69u0r6iIgjYJqMAQRIBRgCCJAKMAkwRkvFbrJvDvs6u+yrvkY0HW8Y1nl35N5ycdXevRu30pHSV5Jq6X1gImBZ96XVNmh+MOFYJ/R/TubaispaRtb27sHHE/OI4X1S0gm3vdgiOQpfrhuaN/V79q4+8yfYqVD5H9OOrtn46hu10NvX5jdVgag4H7gsOEBiQq2rs4TnaapFn95dPFgiHuP2JdxV1d1UxR16cUWCjDpQGUcW7nhQYtZV6+H2SuVveUxeWJ/7y6Oq1adGnfUBbvi77H6edtll2NW2WuVN2v8F01c1GvA+mmbnJJWtkcnStOgJqJ0IDPSvrFwPRNjhcr3MI1BvgFzxnVRY5IpB4MOpFkv2BnwK7oAAFPuOWfxuK5KKc++oXZiU6ELk3QgjLt10+NGrh49uXDhrAnDO+nKYgBAaz8hJByAyv7v0n221VJH8xqnA67vHhnvLpICSwpUg0kI7scwOxmsGkb/HWm/qh6FAeujIyaYfju21KWLvnqLdv3GzPp717nnWWwA4KZ+/MIijEyMCBH+AhIK1WASAtcesizYs03VEOG+2Dd347OK7zBVmxl77k3d/PXp7RvXb9y4fjl6XdS2VQusJu05s7U1SQKGYSIotsRDASYhMEVzB3dPW3qVt1jX7iwNLg8wisNikzhdhqZo2GmwV6fBXvM3ML8nHPnbxzdyxsL+twbq0zifP3zhgkX1SoxMv7ol7IrM8EUz7NRQ/DUFaiJKBc7TNTaK2uNPV33qxdDrNiHY30H2Z/Kzgl4DO+LPY2JecarvRuVciQgI2fe4SA5FVxOhAJMKtDZ97PWLLmzb9aK4yrtUzp2bz1gKba1MzSYscNZ4Euy9PO5HZYxR+XeCQ2KLDV08eskKv8gSAjURpYN876Wbxsa6z+/R+foEN3tLIy1aYeqz2IP7LvwctD3IVROnO205uOiDS9DQzvFj3IZ0M1cveJMYd+rEjW9G3seX95EXdfHFFwowKYG3GLX7zk3b0O2n78ZEHHyfTWgatmrXd82F+VMcWtEBAFPvF3jrWb/wgJCTsZHnduXJ6pmad50ftdLfyUwRtQ+bDuM5qxRKV2nmULqKuED3YAgiQCjAEESAUIAhiAChAEMQAUIBJgmere5ArxyDiBOyaoYWvTzXXfxcKuqSST3UTS8p6J1mbJ9nKwcAwCn8/vzinsgVIx9mXnkQ1ltJ1EWTZijAJAVh0NPV01O54ltvd8uRVlN2h55aYe+lXuVBFreoiK2ggEZmCAtqIkooXLdbDxOClZrygwROwsI2Cg473yVEeHU3tph7gwVkTsK2qQ6dWmmqaJp0Gui9NSHnV14LmXFjg4edmY66vvWAaZF3/xmtYOAjyl9EzKEAk1BURlLiRy6hraNR9i8mv8XM9j2p6rZhh69N8bX5vfr4nefazwnfHT67F/e8Xx+7+dd+UgBQcGNhv6Frn+iPXb9j41Tr96sHz73EFO0vIuZQE1FScNPuRx+jywMAcIp+JF/avf1sock0v9HaGHABgP36g8nlpxH9FIH8umNQ5Ps2i+5eWNOZAQCuLj0VOttu3nBkfh9vOBS481OXtc8OzzUhAMY4WXHaDdiGIuw3oACTFOyH2ya5bQMAAAyXUdFva+9/ZFOAQ0UaF64zaJSdIgBAaVJ8IqfzivEdGeV7Mjp5ebbfFHQrienJvpbA7rh6hHF5Vph8T8dBujvOCPtXkSQowCSF7IgD6afHKtf1Y1xVXRUHAKCKc3KZuJauduXdAa6jp42V5uYU5JVmMXFN7cqJbwgtXS10F/E70F9PWlRMCYDJq6kxyMz0zMqZosisjCxKRkVVUUlFmSCzM7IqezyqfoM0AQowqSNrY2dDPDx44GnFjL/MJwcOPaF16WUjq9TNvhP+6My5L+VBVXL/TOx3FGC/AzURpQ5u6LHEO+KvdSP+Kl46qYd69p0967a8NfEJ9TTEcZi4cnLkX0tHji9e6NSqKOHfLedIdQJHk001HarBpA+mOiDs9rUQB87ljT7jfIKvkkNCb9wO7a+CAWBqAzdfP7fI7PWOOVMX7f3cJ2LbGC1cAU2c3XQo4VIsCSjhkvr57Mzxh0oDxvUrmyKRyj7sbOJdGlZ0fqIgPk4aoBoMqYTJFMQHz/CaHRb3Mr2g4PujQwsDL8oM9hgi6nKJMXQPhlQha/v3ie25k5cMtfJnAyGn3cEl5HyYh66oiyXGUBNRLAl4Tg6Smfsjk62ip62A+jd+E6rBkNpwhloLA1EXQjKgezBJ8HiFFR3jQabL+ldcfg7EvjPPRLbD6mf17sT5Yx8nBVANJinoXWbunNODUe09XKODvoAuoUL+OLGFAkxSEIZ2YzzdFBresE7coqLGTzHw+x8nHdAFRwqUfDizys3OqqW6gqJmS+tBPrsf/qzo2aqdi1nxg6crrRm6k84XVbxBvt9kK6vqdDCLR6cYUicUYJKOyr/g23d02Gv9EfPC92xfMc4y/ZCP06KrVRaBqJKL2eXX8kc0Sycns9yLJ2+Vb8h9F338ocJgz+EaaCJtfqAAkxSlMe6KNTodaK38brPJtBSmucv6g4fWzR3nNm7O2r2BTioZyckZlWN42a8/mGw4EzHXY6h1leihWTk5muVcPHW7BACA+zrq+BOV4Z6DVLH6P064v3Tzh+7BJAWPXgdM0dyMRmhNP3B5OgBQzJzPLx7ei9139yelTVUZI1+Zi1kNzcrJsU3QvyfvlDoMoCVHRSVrOa7v/2uGqro+7k//WuIO/UEkRZ29DlRu4tb5CyOvPHmfr9i6Y5dOavKM6q28X7mYNdDaOTm2Cfrv1D1mb+XjUa9bjNrSu3IdI9TJ0TioiSjhyC87XQcsvKfvHRn/JSv12c2TkbN61Jwosa7lmWntRjm2Tj93Mv7e8RMfjFw8ejJ4bobUAwWYhOO8fPC4tLWrv8+QdtoyAMD99up1XmM7AmntnBxb/zi5fOHRL63HuNvQG94DqQE1ESUFN/Ve9DGsRh2Da7Vva9NB9tDBlWuMvPu05LyN3RW2/wmQyg/jX2YZWGnKNHBQmvUoR5OgwESs8xo362rnSh0f13Fovzao3VgFCjBJwU7cMt5tS403ZezC3lzdcyh11rJ//Ny2qpt1Gz7r6IOFMV4TI+bN7WobO9u0oaPSrP8a3irog6b7GLPq437r/Lg+bRRQs6gSGk0vloS2wiWV8d/I1jMKA1/HzWqJ4qYJUA2G1IFklZbkJYRujoN+20YbouhqGhRgCG9kyvaBZn63OcrdVu1y00PDN5oIBRjCG67vuf28eb5Rjx6mKijtsslQgCF1oGu1GzBY1IUQe6hpjSAChAJMEhwZJUe3DnjC4Wsn8tvdYwdjXxc1sBnKX/4tqIkotTjP986e8m65/UDzhh9cofzlpkIBhjQCGtrbVOgSJOl4pjOTH8PslAb/k8G8Oft/DMvljzgAzE+nl7vYWeipKGub2nqsOf+J1fCxkQahAJNodaUz4/+bEv1iv5sGo9uqO+/iFljBu51O3Vwi0ywnBf0TucZNO2mDU99ppzLR7AC/DTURJVp5OnPofh8rGgCAq2nqldHJyRnkACOdltqKBMiqG7TUUy06P291nJrPlcvhvRUBwMV1kP6g9nPX7Frw13JLACjPX3avdmjCeO6NN2F2aIR9/VCASTTCoqF0ZgAA9tO469l6A/sY5ael5Zft19HOnAp68KgALBUBUP5y06E/kWRrMJ0ZAICb8T2Tk7LbyWh3tbdl+uQXkKAIgDo5mg7dg0myxqQzAwCuqKxI7xz4gkNVw7w+C43x/V3oDyjJGpnOTO9g10325dlTLyvmHaVyzs/uauWxLxUtH/u7UBNRQlB5L2Kjjr2pcsHENTsONq8nnVkZJ3Ay9UHcrcf9bUYtmb15wEqHIT8WTrLX/fn0/N7tUVnDDg9qgQOQACh/uelQwqVYqpFweWSUnMfJmtNey9iGvrrlS5wPmLXsv/iPpepm3YbPWudvFOM1MeK56eqEWF+1ayvcZ++6+9102a34Je2Kn+5dtmTHxQevM3Dttr3HLglc7NhaDgA4j1d06Lr2BY9hWDJ2YW9uzjVCjaD6oAATS0LLaEZ+E7r8IIgAoQBDEAFCAYYgAoQCDEEECAWYJHi2ukOVnEickFUztOjlue7i58YvqFeGTInow8AwetslD2p2G5KpOwbI4xittf99MVtChfr57s7l2CtJqUxeP/y+c4AsRrdYmsRfuioAUNkJ2737ttVXVdIw7jh8waHknzz6C9FzMElB7zRj+zxbOQAATuH35xf3RK4Y+TDzyoOw3jzGbjSA8/5k9KO/u3StMpKX/HY2+m4pJY5XZO7bvd7D1n/svePTlem1p8eSMejUbwBNz1SZz4mzqB/HZoz0PZGr132kk+6H2LOh459lKjzc56hVY2WN3yo60nwQBj1dPcuMn7YgJCZu81CFd7tDT+VUv6w2Yp1YumUHsy8xJx5WrajItDMn7qu1a6fN3wlDcrl/JOWF83RVezom03XqMtd2OsoqLaz/WnXlTfxG184t1VR0LIevikunAID5LnrRiI7/01SUV9FtbTs2+GYmBVD06X7Cx0IKyOyXN++9S1rfVQaT6f73qX99+lkMj/hMAiv10bW4q/fe/6S477b0U8FxRvuARywoifdrTcMI7VEHv/EczkJlXdh/NgMzmXn0+vH9Mdcj3bWo1BN7L9UaJ4MCTELhut16mBCs1JQfJI91YsmchG1THTq10lTRNOk00HtrQk6Vs4gwcXLukHryxIPKlEsy7Wx0gtaI0T1kq1yf6zoIJ2mphULfjee2uVlqyNJlFHXM+8888KKkgb0agZ20N/KVtlUruZzkc38PsRoQ8lrV1JCR9+r82unB99icZyHuXsHnU5S6Oo4Z3Ko06fDiMf7nCrgpR/38jn3lAvtJxLhZh7+QAEB+2DVjRuS976zqlQ3Renr4wi6y7OQd66Me7l/37wdSpd+qYPcWvGOE1Os5dvzE6SOtZQBATkdXBaO4TGat1jMKMAlFZSQlfuQS2joaZf/iKuvE2hRfm9+rj995rv2c8N3hs3txz/v1sZt/rfIOgmjl6Nwp7VRlhFXEV/fKwVJUfr0H4TwNmRyUNXRjdOzZndOM3uzyHhv8lNPgXg0gjGZEJV69mnBkigFBQcvpUQlXryUenKCLc1Nfv/1ZmCvXxXPqqv2Xzx3cu2+TuwlB5rx5kw5tl9y7u6QtDRj9d3x5uNySAACyUHfc5R+FuZdn1RiGImPtF+5rQcs+6Tds+eUCua6LQqeY1DEnJKYzZPnuvbvn91bGgPX5xJbjH0n5Lg72tRbYRfdgkoKbdj/6GF0eAIBT9CP50u7tZwtNpvmN1saAC2XrxF5+GtFPEcivOwZFvm+z6O6FNZ0ZAODq0lOhs+3mDUfm95nWouxYhLHj6E4rIqISNtj2kgEg085EJ2iPXNmdcaLi08jUw+vrOoguAJA/lVyjTwf3VQCA/hY5N1svevyiBNrl1b2XQcPXesLIvDUDgFRSVsSAZmzeWhaAo6ysgEEOl0up9PZdhu2LPOjbf2nCgxffirhA5zlMCYAwG+Fpq8kzcuS7Lw2bfGLozo/ZdKtF4XPbNbT8DJAZN9Z6uK+5lmfkvvs/3za1DopqMEnBfrhtklsZL++FO+/T7P2PnAtxUCu/pFauE1uaFJ/I6ew1vmNFdcTo5OXZnpN4K6myl40wcnS2+XH6xD0mAJCpZ6ITtKvVXw0eBFPvN9y2fBwwrqmjhQNJUo366Ppg1ZYKrL5sIJV3caZd/2lB59JaDPaL2OXToe5ca0xWXq7OLg2SzSYpCoDisNgNNF6p/IdbXXsMXnWL6B94+d6Bsa14fCQKMEkhO+JAfnkiF8ll5qY8ObthdJvKJV9/rRNLFefkMnEt3SrdFbiOnjZWmptTVHm9J/7n6Nwl41TU3VIgU89EJ+qMdO5W5Wre4EFwdU31WudWfXv99u/PeXLhUiqXMTgo9lDQfFdDdnat6OBdnVVXeOvvef99wVsY6pBvts3Z+LCeDiFmcrjTwDkx6ZZzziSeW9JLi3cooQCTFhUXf0xeTY1BZqZnVp6AZFZGFiWjoipf5bKOtxzp3DXrzIm7xWXxNbpr1dZSwwfhVUPUt9dv/364rr4uAcy4VaPGeY/pN35vKgnAYbEBAJNXkMOAnXxs/e479c/jU/Jgw5wdb7m6bhEXNwxXYz/ZNDviZV0P/fIvbFh3M5ciFLnJmyf/NWTIkCFDRiw5n4N6EaWerI2dDfHw4IGnFV0YzCcHDj2hdellI1t1M9xwpHO37DNHjxyLfqBbI74afZCmfXSTEGYztqxzslTMenzzCYzcGjhUHuMkx8S85ALRxnXOGGv1gsQjx5Ny62n1sZI3zw57xpLt5rd0pKXbsultacX3Auf+85Hn9MWct4kP80igOOlP4y6Vu/zga62mLurkkDq4occS74i/1o34q3jppB7q2Xf2rNvy1sQn1NMQh6rXX9xghHP3hUsXri/VnRjYRabxB6l7Pu369qoXrf2qp+xVFd/YrHvJXlf+Db178DtOcNnXmvOjn8//tc9o/19fth534Om4A2Vfz2Mtq3pkTG96XOn08m8W3ytaXPGDLoHJrMB6StRl/Sv2+vpLDYBqMGmEqQ4Iu30txIFzeaPPOJ/gq+SQ0Bu3Q/ur1GzV4fojXHqycn8ajBxtU6s3rbEH+RN7iTOUcCmWUMKlcDDPTjQcc7SgVohgiq5HU/8bweC1T3WoiYggdWL8tTejeO/vHIF3gPV9eel3DtrcXLdAC8khooHuwRAJV/Imyn94e0M1JQ2jLi6rL33lOy3lt6AmItLsvX8P+fmN3VhFBUxNK79l3ls9avKFTmt3XumjnnJuwzw3T6X71+eZC23VaRRg4o9MiejXevZN0nzx3efru1T7j5KpOxzazLzKMllw+2Vwd7FcqOHTJ2jdmr9dPn4EY+OyL7kpt298Nht7YuawtgTYtF1059+B1xML5pmr/vmC8oaaiBKD8/5k9KPq4w4qsiTFWXHx7+xCGNj2b51yOjLmUVrWl/uH9sQW2PSz4T8DtelQDSYh6JYd2nyIOfFwTdfKiqoiS1LpVUl9u9ZEcrkYQTSjR1OmpqCiAgCQnw/v3ze8TVVyPVcdXnCj65jO4RQArj54W8IsC6G1DwHVYBKjUVmS9SQ7CixL8nd9/Qpv3kBSEiQlwZs3oKPDYxsdnWrbfP366ydkatQUxy1y/udefs9Ke3JsXM7yYXNic4VYp6MAkxQNZkk2nOwokCzJ3yUvD2ZmYGMDNjZgZgbp6Ty2SU+vto38r6HD5NeYrScYE4KXDW2rq9GivfOG9a7FB3fHFgql5ACAmogSpIEsyfpSJMuTHQWSJfkH1NUsbMQ2GIYBl/trdCTFJSkME2brF9VgkqP+LMlGJDsKJkvyN+XmAgaAN/qFAeTmVuyMGzhOdsiN9FsW/ehTyru7+/0WHWW4TXZQFEbBy0sgvI9CBK2+LMnG5FnynSUpjEaiuhrIESDb6JccAepqlUU1HPvvuQ3WjwJGdLTo5h6WOiDyfOhgNSFWYaiJKEnwliOduy4JPnF3o8nL6ESdkX9XZnGVJTt+Ts8kQbk8VMqSHVtVybOsO0uygR0FiMBAgcazZLxRANV6QDG1zlO2XZmy7c+XrFFQDSZR6smSbHKyoyCzJBuBwECBDvKMxr4U6NCcHjGgGkyy1J0l2eRkxybv+GcU5IMcg78arKDR46oED9VgEqbuLMkmJzuKNktSTR1kaEBv9EuGBmrqQilZo/BOuIRti4ReEgGSvHQVKUq4fHQfpjtD47vWKQp2noBO3QVZJj6gJiLSvBX+BAadd/8LbxQU/hRgefjEO8Ak75KPiCsVNSAI/gJMRa3hrYQF1WBI84ZhQOezm16oQzUagAIMad6KCoBBg8Y/0sYAigoEWB4+oV5EqSRGK1kqKwNOA1qjXzgNlJWrHYHMvBHkaW+uo6rVpr/v0TdCGeD1CwowaSYmOZo0HIhGv2g1TunShNVDRv+Lue+8fO2Aj2bs1LEhz+ueGVUAZRfiZyECx1eupHjkaGIYEHyepVXvwfLPhm39MfrwrRl95AGsI8JyFz74mk210xbWbRqqwcRfA7mSmfGbJvRr31Jd3cC6j+e6q99/Xb+b7UqW1ZQUgIERtLGCNlZgYAx0Ou+XgXHFNkZQUnkPxn508y70GdpLHkgWi4NpD1u9b9VQoUUXoACTFHXlSmZfnGnnEHBf3XHFjl1r3Vo82zCsl29sfnkLsLmuZFmNqgaEHoXAfyHwXwg9AhoaQMNqvjQ0IPRIxTZHQVXj197FaV+zVahHywe0UleUU9S0GhV47YfQkrEBUBNRUvDOlbRK+2fV3rSeIc+PzTImAMCpC/m2U8h/V4MH2gBAs13JshoOFxaPBQVFAIDiIij6CbRaJ23RT1jiBfIKAABFhTDp1zgkilnK5H6OO8vce+rdKaPiBxGTx7hNN3gUM144maKAajBJwTNXksq+ff0Z9BzjYlQ+zQvNcuGN7x93DpOr2K2ZrmRZVXEh5GVC2idI+wS5GXU2EXMzyrfJy4TiX1MCYPKKCoTyiOVBrtZaisr/67twhZt8XPR1IY70QAEmGXjmSpJZGVmknK6eauU9h4yiuroyo3JLoa9kyXcjUVEZMJy/l2JlN72sRbvWUFTELP9YLpPJpsvLCbHdhgJMQvDMlVRRVYaSrMzK1UGovLd3rid+Kqw8zYW9kiXf/QsYAI2f0fS0asM+aFbjfXokrJ4Wce315/cJB+ctPqbkNdVBgd9CNB0KMAmG6/S0MyPvnDiVVn6mcz/smdT/r79vVu2Cb+4rWZYU8fGUuexVUmXFZ9zY++j5uQpRPr3bd3EJSXXYczaonzKaMgD5I2jWM5a77BvrN3hs+gJnK8an08FrkowmnXfUxKrchTSnlSx5kFcCgs+ZQuWrTd2Lqdj4/hfvy/cH/xmoBpNouJ7rvnvnFlqlHFo6ceycHcmt5hw/H9RftfoVvHmvZIlhQOBAIxr7IvBmNdgXrXAplqQo4fJVEhwMBb5G+46dB21tBFgkfqAmItK8ySkCjvOXDyYnxHkPG1LHCpfX/xVyOQTqet9Joi4C0mQY4ARgja7BKL6iUeBQDYY0bxgAgfPTWUA2p/hCAYY0c6XFQKvV9dLgLs0G6kWUYOz7/q1pWAWckNcx7zls/IpDz/JrNriKP1wI9hndv7OptpKStrG1vXvA8eQ8oQ6KrZO8YnmWVyNfBA7yzf4eDJEcMt1m7/LtSgegmDmfXyRePBo0Lub8k9NxG/uplzelCu4HDhsekKhg6+o80WmaavGXRxcPhrj3iH0Zd3VVN5GfqxjG96Q3dXTTFzzYs/GRxcJpPdAKl8ifg7fs5e7p/Gv87uL5Hn5DRoVPW/PXszB7OQAq/7K/x+rnbZddjlllr1XeoPFfNHFRrwHrp21ySlrZXsSnCLMEaDT+AozJI1mUyr2y2HPGHuNts6b2UEL5YAh/6s6qrInWYsi6tWM0Ph3850ohAJApB4MOpFkv2BnwK7oAAFPuOWfxuK5KKc++ibydKCcPBA1wvLEvggZy8jUPQmWcmTczJl9B+N0fKMDEX/1ZlbUp2Tv0lM1LvPuKA1TujUv32VZOjuY16ilc3z0yPn6PV0vRnyAYYDgQtMa+sNrd9OS3Y7MXvPYImdpKmKszl0FNRLHHfVNHVuWgv+rYQ17fQIO6/v0HF7ipH7+wiNYmRsI/8xqLyQRNPZBhAACwmPAzm/dmyhqV2zCrZZ1xP++dvvT71DP/djx9TtCFrQ0FmLgrz6rcXD2r0odUkKt/vzIkSYJw11Tll4IijJlb3m9BUXAoGEpqLbEsV32bzNTKH7HfbPdeU+wX62fFeHtaWGWuAgWYuCvLqrSomVUJAFDXvIYl39KyMR09HQIIvZb6NM7nD1+4YFG9EiPTr24JuyIzfNEMO2EuCFkbyYUTEcCQBQBgMYFVwmNwPasEoreW12DMUug1ouIH3Ddbp25gTT/pqpmfnZ1XzKFYhbnZeUpqqvLCqrJF38RGfk9jsiqrK7wdd69UtWtPCxpgWn0GdsSfx8S8qjH/KJVzJSIgZN/jIjmR124YFBdATibkZELhT8BpvF+FP8u3KS6ocg/Gff8s+futJd10NTU1dWzXPS2+Ma+tnu26pzVnWxUcFGDirlFZlZW46XEBy49kGnlMHqAIAITphAXOGk+CvZfH/ag866j8O8EhscWGLh69hLKKZX3YpUAQfGRbEgSwSyt2lhm2N5ukynBerO2s4BD5g/VibSfhNdxQE1Hs1Z1VCR8AgPx6N+oYlw5AsXK/vEy8eOhQfE5bv9Mr7cv6sjFNpy0HF31wCRraOX6M25Bu5uoFbxLjTp248c3I+/jyPrU6vIWOIQ8EDXiuYscThgFD9KX+pY4F+AK8hF4SAZK80fQ188HYaZc3zP/7yK3nXzlabe09lwctHmEiB+z7/hZ2Ie/Ln4lhuJymabvOXfq7L1jo1aF60iU77Wp4QMjJhBevPufJ6pmad/nLd6W/k5miyNuHAJmpcDWKvwX4+ruAloEgy8QHFGBiSYoSLtM+QMIF/kZydBsK+iYCLBI/UBMRad4YcoDx2eXHaNQTCuGoI8C8/IRbDAFLbUbLziP8KVv8AS3AhyACwWYBjcbfPRib1fBmwoICDGneZGQBJ/iY9AbDQUbkzxYqoQBDmjcM43vSm+bUREQPmiWbRCQ1E3Q+RtMT9IYPKESoBuWzqHEAABLvSURBVJMCYp3UzGUBQfB3D8ZF92CIQNSxkqtYJzXTGUDjcyQHnVH1Dea7qJWLN5+5+zwN9GycFm5aP7FDU2YYbiLURBR75OfwXgodF+0PH2OpIUuXVTfpMmzOgZdFde8gZknNGGAE0OiNfWHVJ/BgPVgzavwB5rCQS48eRC8xuTNn5NxzWUJc4x0FmETgvtk6Y2lSq2nh//0T6N7y4z8T7EZsflVXtgqIVVIzyQF6HSPoeb7oNCArhy1znsZEf+69es/ioe1N2vQcv3m9S2n0/mv1XH3+NNRElAhUKdhsunTSrzUNADwdzZzbTdoYes1796C67vjFJ6mZJgOySuXLxnI5wKxjzsOyMcEAwOFUnUcR0+jls6HPAK3yOo3L4QJdTpgL8KEAkwwydp4epuX/TFzPZarTwnN3br3iDLJueNdmntSMEWBtV9Hqo+D5bR7Pkeky0K7KNoWVizMRrYb6ziz/uvTtgRn+J9XHn+0nxOdkKMAkAiav26LK+Hi6vqEulp2RVffdk/gkNXPZ8DqpPIuZywWKAlqtapmiqm2jZ1xzA3batc0LZgdekXXffXZ9byEucInuwSQDVZz+o8qTLU7G9wxKRa3uzjIxSmqm0YHDBFYJsErKu+x5vris8m04zBoRyE057dero9sxpZnnk+9tH2PKqOuTBAIFmGRg3T587FN54heVcSoyJl21u50l7zsw8UpqLh/sSzT2RVQfuMhM+ttpylXrrXfjI2f01BX+Q2jURJQMNCwpYIhL5gJXS+ztqfDgE6Xd1y8YrFQ+741YJzVzuUDQ+RtNz62cdrX42o7IFNtl282K3jx9CgAAGKH2P8uWQnsShgJMImAa7ruPmJ9bHjp3SzrDuMu43Yc3TLT+1ZfGuh/m5QbwK6nZfv7e6knNmHq/wFvP+oUHhJyMjTy3K09Wz9S86/yoZpHUTKMDzk8HJwZVmojc1OcvsrMSfLtXztiGKbpHZx12ElZDsY6M5nePhPT5QnFd4vLBqmY0k5/De5sHWZ79snMgn8v8iIXSIvj2gb8arIUJyAqzI6M+qAZDmjcMgOBz8QdRV7pV8Q4wybvkI+KKJHn0yze4S7OBajCxh+u57YrvLWfWvNI0/hiCDgQBVKNrJYxqVhkrKMDEH0PXoouuqAshOBhgBB+PkyhoVougo+dgEiDvwAg5rDKrEpdR1mvT3XXVmQ+8J/cVMyTQZfgYTU+XAUBNRORPI/43eu0aJ0McALglOZ/uHd6+1nlI5rmErQ6iXbvht+EEryW/6kHx160vYCjAJASu1n64h6dVxak12as9y2z0/n/ighxcRL7M8u/C+XzQ3JygAJNMmGILfTUcw3Hxrr7K0Gn8dXI0J+geTPKQzLyPN0JX7/9i5DWpfzNaB6FpcBxwAmhYY184AXi1s5oqeLJrSm9zHXU9ywG+h94I+b4U1WASgv0koB0toPJ7TKnL0ovrBqqKfw3G57RtGFVtY+rHkYmDlqRP+vfidv3X272nD56j8WTXYOFNyoECTEJU6eQA4BSmJp3YvmlIP9bpuKC+Yt7LgQFB56PhR2FVA4xMiYq8pDnj5hrHTjToFLLxxinXXefWD/LUQIN9Eb7U6OSA8RMGqHTpsWn1AZ/es43E+UYAwwDn8yytMryW9SzpuUKPxe3KjiDXzd6GHfDwNcfTVljPosX5T4/Uh2HVtb08+9P7L9yGt23OmjCZQeUuVFFWFlNdS6PiNJfT0JTPzcwW4nMyFGCSivXq4fNiQv9/+s3ooZAo1FpthRTqUEXURJQQZN7zS8ePvai4B0t7FL11e7KW6/FxJtJ8DcUUNDUZeVk5FSHFzMkuUTfSEOKfBAWYhOB+jvL3iCr7GsNl1Vuad/M5GPL3KC3x7uH4XTLWNlYF/957zXGwpgEwk+49prV3tkDTtiH8UPU6UyJRa/7+Obihy9TB6/yXbRsS6aX7asvKY7jrf8PVhXjRkeb2AyIFcD2PvReWqUd5tTfp5nvLKvTSlqFCfTbIe8qA69evC7EMCN+kaBF0MYdqMAQRIBRgCCJAKMAkAPfZ6g70KhmXhKyaoUUvz3UXP5cCsO/MM5HtsPqZmD9vFleoF1FS0DvN2D7PVg4AgFP4/fnFPZErRj7MvPJgI/oXixL660sKwqCnq6encsW33u6WI62m7A49tdj/D30AxWGTBL32+plIfVATUULhut16mBCs1JT06r3EJR/OrHKzs2qprqCo2dJ6kM/uhz/LNyh5E71sdFcTHSUFNQOrgT7/PMynAICTtNRCofeKPQv7GCgxGEr67Qf5Hn7780PU/CEd/6empGFiP+3ga2bDB5daKMAkFJWRlPiRS2jrVH2qSuVf8O07Ouy1/oh54Xu2rxhnmX7Ix2nR1WIAKIjzH+axM8Xca+XOyPXe7bMPzxi1MLZ8nS3W/eDFcSYLD186u9VV4cH2SfZt+wdmDVweeThivO6LPT7+R9Kp+g8uxVATUVJw0+5HH6PLAwBwin4kX9q9/WyhyTS/0drYy1/bkGkpTHOX9aH7faxoAACupqlXRicnZ5ADDF7FxaWou+z8Z9UAGQAY08NQc8eX0lwS5AEA8O4ronfPNsYBejMSTzjsaTH9xp555jSAvvKPoh0uvvjIAR163QcX63SZ34QCTFKwH26b5LYNAAAwXEZFv629/5FNAQ5q2J3KbQiL6QcuTwcAipnz+cXDe7H77v6ktCkSgDDu2F415Kifh8bsyaMdbK3bT9q8EwAAOABAGHbtalAWJIS6phpNr3tPk7ITh9DQUse4HG79B5dmUnxtkTCyIw7kU2VILjM35cnZDaPb1JyRg8pNjJjUp52hmqpRrwlro96w5RllLUhMy3XXlb0z2n47NP8vG2MNrdZ9p4THp1d07RNEtb4NugzPVSbqPLg0QwEmRcgvO10HLLyn7x0Z/yUr9dnNk5GzeihV/BBTbe+1/vjdz9mZ7+8dD+hXembByBlH0hvfR1HvwaUXCjApwnn54HFpa1d/nyHttGUAgPvt1es8CgCAyjo6zqyNy56vJNDVWnVz8otY7ahZ+Prl18Y/nq774FIN3YNJEZq5TQfZQwdXrjHy7tOS8zZ2V9j+J0AqP4x/me1q09Ugw2+pu+/PGQONqM+Jp/Yc/dlmxjALGrxs+LgNHDzLwEpTElcuaxRUg0kR3HjqnkPzLT794+fm7L3mdKnr0QcxC2yx8/PmHk4znrE/eq0DFhcyy8PTN+RUZqelJ8+vteVjVsV6Dp4ixcO0ULqKWELpKuIC1WAIIkAowBBEgFCAIYgAoQBDEAFCASbumDHuijjGG8Mu7KOUD1USNfQcTNzRu8zcc3A4hwIAKL4dOnN39ohfq0DgWp210SVUpFCAiTvc0G6Mh13Z13nksdl7yOqrQCAiha5vCCJAKMAQRIBQgCGIAKEAQxABQgGGIAKEAgxBBAgFGIIIEAowBBEgFGAIIkBoJIckQUtdNjuoBkMQAZKKGqxvv36iLsKfxmuiB6QZQjUYgggQCjAEESAUYBKj+MOFYJ/R/TubaispaRtb27sHHE/OIxuRkVl4ZJQc3TrgCUfUv4Ekkop7MClQcD9w2PCARAVbV+eJTtNUi788ungwxL1H7Mu4qwEoI1OEUIBJACr/sr/H6udtl12OWWWvVR4w/osmLuo1YP20TU5JK+vPyCwUQZGlBrp8iT8y5WDQgTTrBTsDfkUXAGDKPecsHtdVKeXZNzQth+igGkzsUbk3Lt1nWy11NK/xz8T13SPj3UVTKKQcqsHEHjf14xcWYWRihKbhaIZQgIk/kiQBw9Bad80SCjCxR+i11KdxPn/4UmsNEzL9avjixdtv56JhHyKDAkzsYVp9BnbEn8fEvKrxIIvKuRIRELLvcZEcqt1EBgWY+CNMJyxw1ngS7L087kdljFH5d4JDYosNXTx6yYqwcNIO9SJKAEzTacvBRR9cgoZ2jh/jNqSbuXrBm8S4UydufDPyPr68T2NW0aPyXsRGHXtT5XqLa3Z06d9GYGWWFijAJAKm3i/w1rN+4QEhJ2Mjz+3Kk9UzNe86P2qlv5OZYqPah9yvMYs9Yqq+I2MbigLs90nFCpcoXQURFXQPhiAChAIMQQRIKu7Brl+7Juoi/GFoCXRxgWowBBEgFGAIIkAowMQf9W1HfwYuYzHvVvXMLu674O4MFa8zTACAvAMj5GQ6rkmuOp6K9eGgeyuGXNsp0V9RNrOAoACTEBT79bZZgfeKG70D+9ORSYOmnGZ4Hbq8c7ShVNyLiwIKMAlBa9XW+H34zKCk0sZszfly3HvQxBgZr0NXdo1C0SVAKMAkBM1y9pZ5Zq9CZm56ymxgU87X6GmDxh+njTt8eaeTAcoiEygUYBJDvuvibb7GTzfM3PKCXedGFCftlM8gr0PgefjyDkcUXQKHAkyCKNqu2Dpd/8HaWdvf8uy0oLhpZ30Hef73gcMpZpJ09L8XAvRHlihKvVdtmaR5Z9Ws3R9rpV8CcJMjA2K0ll+7E9q38Ogs36NpaDYcgUMBJlkw1YFrN49Vvr5i9n8ptcIHU+658vzpxbY2M3ZtGMiKmeuz/wsKMQFDASZpMI1hG8LGyMYumXs4tUYtRhgPcrJRxgCIVlN2BA+jzs+fvvsDj5oO+XNQgEkeTNtxY7Ajdnahf0xGXTUU/r/x20JH0q8s8t76uu4uEeS3oQCTRHiLMaEbhpKPH3yqu37CDTy2bnZWuLViSthzlhDLJmVQgEkm3NArPNBBrd5/L67nujnCXfX+6skbHpUIq2DSRioymiVP374oYUU8oBoMQQQIBRiCCBDvJiKCIH8EqsEQRIBQgCGIAIkiwKj8L8nvM2s9e6EKU1+++lYkLi1WKu9dwoOPPymgsl7eeZzaqDQsROqIIsBYV/x7jqs9VI7zOGR472U3xWVcASt+7VDHoPtMYN1YNWTm0VQ0qg/hQajJrAWXFjkG3mVR2a9L0pLce5+utigB9+enZ1/lJimIy0og9LadrPLmu5jdNSZSizPujux8SKbWNoyBwbc2Dqj9PiI1hBpghIqBmbk5m/vp24NsrVZm5srVggmz6j7OaZ4dXZgl+g24qc+Riwp7zr/MfHH+ValO196dVWtdG+iWWugmV7qJopuedW350CMW+3Z5GEjE2ce+EzT2VJvwICc9ifh1kD8KPQf7U9g5bxPiE998L2zRf0pvtVxSXUsRBRwixCYi9+WJDVEv6p+Aj2bpstjZQuxmimC9PTDd2fe/5HySAlmXqLFaj/s6nOocemLnhLZyoi4bIlJCDDDOp6v7/jlXf3e27HCbBWIXYOwn692mHqdcI64s7HjPe/AzoFlO3jA1fsJ0j6D2Cas6oj4OaYaaiL+Nk7DIsk+cZ+K9gHa0z+G929+dk3HcmUF+DLO3jOh65U2o2HTbIALQbG4TyKIvd44Ezdt6V1yeg/3CTf+WzrDo0KZ6TYXrtzaVy87IRo/HpJvIA4yd9fz8jiWe9ia6rXp5LNkZ/03szkiakalR6f3Ld35We7cw6UZiiaGRoZg1d5E/TFSzJpOFn+6cPnr48JETcclZbExe32aI7ywXV+dh3RkiKlGTEVYTZg/cOt1jOG31Ivu0ErIk4+2D02f+9t2S2iVobHs0LbWUo4SLmf7kzNaFbrb/U8AxwORadLBsQVMefTiHK+Ry/Flk3uO9vr31GRVPmjFcua3z+qvfOKIuGCJqQuzk4CSFOU0IjH2ZzaFrWvYfNcbNzW2kvcEVd/Wp8se/7xsudjVXLcycz2/fvPuSjWkam1uYGSijygsR6nOwz/fiXuTKWU8M3R8+qX35MKmGFioQJwx1o3Y9jNpVvlGamcHS1FYWl9GViAAIMcBobYd69X8adXOft82pkP4uXuPGjXXsqS28zxcAzo/4PRGHbr78ztHqMNLHz6ODKifj6ZXYe+/TszJ/fHsZd4q+/NNRZ/Gvm5GmE3KTlCxOTTge4juyow4DwwhlU/uuRjQVl2N5pJDL8QeQWacmGNIwDJdV01KXI3DlnoHn/nXVp2EAABgmo2LYru/f8SxRFxMRKWEH2C/srOQLO5Z42Bkp4hhGKLey91y87czjH6WiKg/fOG+CujNkLKad+lxKURQr9fxMK3k6Xa7DzBPJGcUckhTDSwby54kswCpwCz7eOrB26qC26nQMMAX3GHEJsdLTY1VkbEM/VvR/cj+F95JhOOz6gSILqSTyB824onGvsct2XXr5LSXpZJivvfjkfLCYTFxTS6OivLi2jhaOqajXzgpDpFjz6Upm6HZynNNJ1KXgF4bx/hpBAKAZDJVCEEnWfGowcUSxi/Pz88tHT5YUswHw4vz8/F/98hhdQVke/YmlGUpXaSrmCVdVl6gG0ttcovKOo+dg0gxdXpuK1s5z7YbODSRom7dDf2DphmowBBEg1MmBIAKEAgxBBAgFGIIIEAowBBEgFGAIIkAowBBEgFCAIYgAoQBDEAFCAYYgAoQCDEEE6P8JbsWG7XPyPAAAAABJRU5ErkJggg==" /><!-- --></p>
-</div>
-<div id="enrichment-with-somatic-variants" class="section level2">
-<h2>Enrichment with somatic variants</h2>
-<p>We get the number of 2593_G&gt;A cells that are also mutated for a different somatic variant.</p>
-<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">somatic_variants &lt;-<span class="st"> </span><span class="kw">c</span>(<span class="st">&quot;ASXL1.G642fs.1&quot;</span>, <span class="st">&quot;ASXL1.G642fs.2&quot;</span>, <span class="st">&quot;TET2.S792X&quot;</span>, <span class="st">&quot;TET2.Q1034X&quot;</span>, <span class="st">&quot;TET2.R1216X&quot;</span>, <span class="st">&quot;TET2.H1380Y&quot;</span>)</a>
-<a class="sourceLine" id="cb17-2" data-line-number="2">variants &lt;-<span class="st"> </span><span class="kw">LoadingRawMatrix_typewise</span>(<span class="dt">samples_file =</span> <span class="st">&quot;/data/MPN/exp/scRNA/MPN_mutations/SIGURD_paper/sigurd/data/MAESTER_Reproduction.csv&quot;</span>, <span class="dt">patient =</span> <span class="st">&quot;BPDCN712&quot;</span>, <span class="dt">variant_use =</span> somatic_variants, <span class="dt">matrix_column_separator =</span> <span class="st">&quot;</span><span class="ch">\t</span><span class="st">&quot;</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb17-3" data-line-number="3">genotyping &lt;-<span class="st"> </span>genotyping[voi.ch.sigurd, ]</a>
-<a class="sourceLine" id="cb17-4" data-line-number="4">genotyping &lt;-<span class="st"> </span><span class="kw">Filtering</span>(genotyping, <span class="dt">cells_include =</span> <span class="kw">colnames</span>(variants))</a></code></pre></div>
-<pre><code>## [1] &quot;We remove all cells not in the allow list.&quot;
-## [1] &quot;We remove all the variants that are always NoCall.&quot;</code></pre>
-<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">variants &lt;-<span class="st"> </span><span class="kw">Filtering</span>(variants, <span class="dt">cells_include =</span> <span class="kw">colnames</span>(scrna), <span class="dt">fraction_threshold =</span> <span class="fl">0.01</span>, <span class="dt">reject_value =</span> <span class="st">&quot;Reference&quot;</span>)</a></code></pre></div>
-<pre><code>## [1] &quot;We remove all cells not in the allow list.&quot;
-## [1] &quot;We assume that cells with a fraction smaller than our threshold are actually Reference.&quot;
-## [1] &quot;We set consensus values to 1 (Reference) and fraction values to 0.&quot;
-## [1] &quot;We do not set fractions between 0.01 and 1 to 1.&quot;
-## [1] &quot;This way, we retain the heterozygous information.&quot;
-## [1] &quot;We remove all the variants that are always NoCall.&quot;</code></pre>
-<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">genotyping &lt;-<span class="st"> </span><span class="kw">CombineSEobjects</span>(<span class="dt">se_1 =</span> genotyping, <span class="dt">se_2 =</span> variants)</a>
-<a class="sourceLine" id="cb21-2" data-line-number="2">genotyping &lt;-<span class="st"> </span><span class="kw">ClonalDefinition</span>(<span class="dt">se =</span> genotyping, <span class="dt">variants_ls =</span> <span class="kw">list</span>(<span class="st">&quot;chrM_2593_G_A&quot;</span>), <span class="dt">grouping =</span> <span class="ot">NULL</span>, <span class="dt">identities =</span> <span class="ot">NULL</span>, <span class="dt">explicit =</span> <span class="ot">TRUE</span>, <span class="dt">explicit_not =</span> <span class="kw">list</span>(<span class="st">&quot;chrM_6243_G_A&quot;</span>), <span class="dt">explicit_min_vaf =</span> <span class="fl">0.01</span>, <span class="dt">verbose =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<pre><code>## [1] &quot;Explicit clone definition.&quot;</code></pre>
-<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1">genotyping &lt;-<span class="st"> </span>genotyping[, genotyping<span class="op">$</span>Clones <span class="op">==</span><span class="st"> &quot;C1&quot;</span>]</a>
-<a class="sourceLine" id="cb23-2" data-line-number="2">res &lt;-<span class="st"> </span><span class="kw">VariantWiseFisherTest</span>(<span class="dt">variants_list =</span> <span class="kw">RowWiseSplit</span>(<span class="dt">se =</span> genotyping))</a></code></pre></div>
-<pre><code>## [1] &quot;Testing Variant: ASXL1.G642fs.1, 1 out of 6&quot;
-## [1] &quot;Testing Variant: ASXL1.G642fs.2, 2 out of 6&quot;
-## [1] &quot;Testing Variant: TET2.S792X, 3 out of 6&quot;
-## [1] &quot;Testing Variant: TET2.Q1034X, 4 out of 6&quot;
-## [1] &quot;Testing Variant: TET2.R1216X, 5 out of 6&quot;
-## [1] &quot;Testing Variant: TET2.H1380Y, 6 out of 6&quot;
-## [1] &quot;We remove the NA P values.&quot;
-## [1] &quot;Adjusting P values using fdr.&quot;</code></pre>
-<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">knitr<span class="op">::</span><span class="kw">kable</span>(res, <span class="dt">format=</span><span class="st">&quot;html&quot;</span>)</a></code></pre></div>
-<table>
-<thead>
-<tr>
-<th style="text-align:left;">
-Variant1
-</th>
-<th style="text-align:left;">
-Variant2
-</th>
-<th style="text-align:right;">
-P
-</th>
-<th style="text-align:right;">
-OddsRatio
-</th>
-<th style="text-align:right;">
-Cells_Alt_1_2
-</th>
-<th style="text-align:right;">
-Cells_Alt_1_Ref_2
-</th>
-<th style="text-align:right;">
-Cells_Alt_2_Ref_1
-</th>
-<th style="text-align:right;">
-Cells_Ref_1_2
-</th>
-<th style="text-align:right;">
-P_adj
-</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-<td style="text-align:left;">
-ASXL1.G642fs.2
-</td>
-<td style="text-align:left;">
-chrM_2593_G_A
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-3
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-2
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-1
-</td>
-</tr>
-<tr>
-<td style="text-align:left;">
-TET2.S792X
-</td>
-<td style="text-align:left;">
-chrM_2593_G_A
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-7
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-9
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-1
-</td>
-</tr>
-<tr>
-<td style="text-align:left;">
-TET2.S792X
-</td>
-<td style="text-align:left;">
-chrM_15299_T_C
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-7
-</td>
-<td style="text-align:right;">
-1
-</td>
-</tr>
-<tr>
-<td style="text-align:left;">
-TET2.Q1034X
-</td>
-<td style="text-align:left;">
-chrM_2593_G_A
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-3
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-6
-</td>
-<td style="text-align:right;">
-0
-</td>
-<td style="text-align:right;">
-1
-</td>
-</tr>
-</tbody>
-</table>
-</div>
-
-
-
-<!-- code folding -->
-
-
-<!-- dynamically load mathjax for compatibility with self-contained -->
-<script>
-  (function () {
-    var script = document.createElement("script");
-    script.type = "text/javascript";
-    script.src  = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
-    document.getElementsByTagName("head")[0].appendChild(script);
-  })();
-</script>
-
-</body>
-</html>
diff --git a/vignettes/MPN_SIGURD.Rmd b/vignettes/MPN_SIGURD.Rmd
index 1a02e1e..2737f39 100644
--- a/vignettes/MPN_SIGURD.Rmd
+++ b/vignettes/MPN_SIGURD.Rmd
@@ -123,7 +123,7 @@ genotyping_mt <- ClonalDefinition(se = genotyping_mt, variants_ls = list(mt_vois
 
 We now plot the variants of interest and the clonal lineages.
 
-```{r warning = FALSE, fig.width = 6, fig.height = 4, dev = "pdf"}
+```{r warning = FALSE, fig.width = 6, fig.height = 4, dev = "CairoPNG"}
 # Generating a heatmap.
 colors_lineage <- c("C1" = "#563e00", "C2" = "#dec234", "C3" = "#e23856", "C4" = "#7f0073", "C5" = "#006639", "C6" = "#b1db8e", "C7" = "#00348f", "Negative" = "black")
 ha <- columnAnnotation(Clones = colData(genotyping_mt)[,"Clones"],
diff --git a/vignettes/SW_CellMixture_SIGURD.Rmd b/vignettes/SW_CellMixture_SIGURD.Rmd
index d44c7d4..53ac87f 100644
--- a/vignettes/SW_CellMixture_SIGURD.Rmd
+++ b/vignettes/SW_CellMixture_SIGURD.Rmd
@@ -65,7 +65,7 @@ print(voi.ch.sigurd)
 
 ## Visualisation using SIGURD
 
-```{r warning = FALSE, fig.width = 6, fig.height = 4, dev = "pdf"}
+```{r warning = FALSE, fig.width = 6, fig.height = 4, dev = "CairoPNG"}
 # Determining if a cell is supporting one of the two cell types.
 cell_support <- CallSupport(SE = genotyping, VOI_group1 = voi.ch.sigurd[voi.ch.sigurd != "chrM_7990_C_T"], VOI_group2 = "chrM_7990_C_T", group1_name = "K562", group2_name = "BT142", min_mutated_reads = 3, min_reads = 30, group_factor = 10, verbose = FALSE, return_nonsupport = TRUE)
 colData(genotyping)$CellType_MT <- cell_support$Support
@@ -79,8 +79,7 @@ HeatmapVoi(SE = genotyping[,cell_support$Cell], voi = voi.ch.sigurd, annotation_
 
 We now select variants with a higher VAF in the K562 cells than in the BT142 cells.
 
-```{r warning = FALSE, dev = "pdf"}
-
+```{r warning = FALSE}
 voi.ch.lineages <- sigurd::VariantSelection_Group(SE = genotyping, min_coverage = 20, quantiles = c(0.01, 0.99), thresholds = c(0.01, 0.02), min_quality = 30,
                                                   group_of_interest = "CellType_MT", group1 = "K562", group2 = "BT142", group_factor = 5, remove_nocall = FALSE, verbose = FALSE)
 voi.ch.lineages <- gsub("chrM_9117_T_C", "chrM_2141_T_C", voi.ch.lineages) # Replace chrM_9117_T_C, which comes up because it has no coverage in some cells, with another homoplasmic variant (chrM_2141_T_C), that has better coverage)
@@ -90,7 +89,7 @@ print(voi.ch.lineages)
 
 ## Visualisation using SIGURD
 
-```{r warning = FALSE, dev = "pdf"}
+```{r warning = FALSE, dev = "CairoPNG"}
 # Plotting the results on a heatmap.
 cell_support <- subset(cell_support, Support == "K562")
 genotyping <- Filtering(genotyping, cells_include = cell_support$Cell, verbose = FALSE)
diff --git a/vignettes/TenX_CellMixture_SIGURD.Rmd b/vignettes/TenX_CellMixture_SIGURD.Rmd
index a679d69..516e5a8 100644
--- a/vignettes/TenX_CellMixture_SIGURD.Rmd
+++ b/vignettes/TenX_CellMixture_SIGURD.Rmd
@@ -56,7 +56,7 @@ print(voi.ch.sigurd)
 
 ## Visualisation using SIGURD
 
-```{r warning = FALSE, fig.width = 6, fig.height = 4, dev = "pdf"}
+```{r warning = FALSE, fig.width = 6, fig.height = 4, dev = "CairoPNG"}
 # Determining if a cell is supporting one of the two cell types.
 cell_support <- CallSupport(SE = genotyping, VOI_group1 = voi.ch.sigurd[voi.ch.sigurd != "chrM_7990_C_T"], VOI_group2 = "chrM_7990_C_T", group1_name = "K562", group2_name = "BT142", min_mutated_reads = 3, min_reads = 30, group_factor = c(10,2), verbose = FALSE)
 genotyping <- Filtering(genotyping, cells_include = cell_support$Cell)
@@ -71,7 +71,7 @@ HeatmapVoi(SE = genotyping, voi = voi.ch.sigurd, annotation_trait = "CellType",
 
 We now select variants with a higher VAF in the K562 cells than in the BT142 cells.
 
-```{r warning = FALSE, dev = "pdf"}
+```{r warning = FALSE, dev = "CairoPNG"}
 voi.ch.lineages <- sigurd::VariantSelection_Group(SE = genotyping, min_coverage = 100, quantiles = c(0.01, 0.99), thresholds = c(0.01, 0.02), min_quality = 30,
                                                   group_of_interest = "CellType_MT", group1 = "K562", group2 = "BT142", group_factor = 5, remove_nocall = FALSE, verbose = FALSE)
 voi.ch.lineages <- voi.ch.lineages[!voi.ch.lineages %in% c("chrM_8251_G_A", "chrM_7693_C_T")] # These variants are not detected in the bulk data and were removed by hand.