diff --git a/404.html b/404.html
index ba7b1e6..fb6924c 100644
--- a/404.html
+++ b/404.html
@@ -8,8 +8,8 @@
 <title>Page not found (404) • MsBackendSql</title>
 <script src="https://rformassspectrometry.github.io/MsBackendSql/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="https://rformassspectrometry.github.io/MsBackendSql/deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="https://rformassspectrometry.github.io/MsBackendSql/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="https://rformassspectrometry.github.io/MsBackendSql/deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
-<link href="https://rformassspectrometry.github.io/MsBackendSql/deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="https://rformassspectrometry.github.io/MsBackendSql/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="https://rformassspectrometry.github.io/MsBackendSql/deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
+<link href="https://rformassspectrometry.github.io/MsBackendSql/deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
 <script src="https://rformassspectrometry.github.io/MsBackendSql/deps/headroom-0.11.0/headroom.min.js"></script><script src="https://rformassspectrometry.github.io/MsBackendSql/deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="https://rformassspectrometry.github.io/MsBackendSql/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="https://rformassspectrometry.github.io/MsBackendSql/deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="https://rformassspectrometry.github.io/MsBackendSql/deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="https://rformassspectrometry.github.io/MsBackendSql/deps/search-1.0.0/fuse.min.js"></script><script src="https://rformassspectrometry.github.io/MsBackendSql/deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="https://rformassspectrometry.github.io/MsBackendSql/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
 <meta property="og:image" content="https://rformassspectrometry.github.io/MsBackendSql/logo.png">
 </head>
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="https://rformassspectrometry.github.io/MsBackendSql/index.html">MsBackendSql</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.0</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">
diff --git a/articles/MsBackendSql.html b/articles/MsBackendSql.html
index 99315e3..5bc06c7 100644
--- a/articles/MsBackendSql.html
+++ b/articles/MsBackendSql.html
@@ -8,8 +8,8 @@
 <title>Storing Mass Spectrometry Data in SQL Databases • MsBackendSql</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/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
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 </head>
 <body>
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MsBackendSql</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.0</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">
@@ -70,16 +70,16 @@
     if (links[i].hostname != window.location.hostname)
       links[i].target = '_blank';
 });
-</script><p><strong>Package</strong>: <em><a href="https://bioconductor.org/packages/3.20/MsBackendSql" class="external-link">MsBackendSql</a></em><br><strong>Authors</strong>: Johannes Rainer [aut, cre] (<a href="https://orcid.org/0000-0002-6977-7147" class="external-link uri">https://orcid.org/0000-0002-6977-7147</a>), Chong Tang
-[ctb], Laurent Gatto [ctb] (<a href="https://orcid.org/0000-0002-1520-2268" class="external-link uri">https://orcid.org/0000-0002-1520-2268</a>)<br><strong>Compiled</strong>: Fri Sep 27 05:10:02 2024</p>
+</script><p><strong>Package</strong>: <em><a href="https://bioconductor.org/packages/3.21/MsBackendSql" class="external-link">MsBackendSql</a></em><br><strong>Authors</strong>: Johannes Rainer [aut, cre] (ORCID: <a href="https://orcid.org/0000-0002-6977-7147" class="external-link uri">https://orcid.org/0000-0002-6977-7147</a>), Chong Tang
+[ctb], Laurent Gatto [ctb] (ORCID: <a href="https://orcid.org/0000-0002-1520-2268" class="external-link uri">https://orcid.org/0000-0002-1520-2268</a>)<br><strong>Compiled</strong>: Sun Nov 17 16:34:26 2024</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
-<p>The <em><a href="https://bioconductor.org/packages/3.20/Spectra" class="external-link">Spectra</a></em>
+<p>The <em><a href="https://bioconductor.org/packages/3.21/Spectra" class="external-link">Spectra</a></em>
 Bioconductor package provides a flexible and expandable infrastructure
 for Mass Spectrometry (MS) data. The package supports interchangeable
 use of different <em>backends</em> that provide additional file support
-or different ways to store and represent MS data. The <em><a href="https://bioconductor.org/packages/3.20/MsBackendSql" class="external-link">MsBackendSql</a></em>
+or different ways to store and represent MS data. The <em><a href="https://bioconductor.org/packages/3.21/MsBackendSql" class="external-link">MsBackendSql</a></em>
 package provides backends to store data from whole MS experiments in SQL
 databases. The data in such databases can be easily (and efficiently)
 accessed using <code>Spectra</code> objects that use the
@@ -116,7 +116,7 @@ <h2 id="creating-and-using-msbackendsql-sql-databases">Creating and using <code>
 the data should be imported as input parameters creates all necessary
 database tables and stores the full data into the database. Below we
 create an empty SQLite database (in a temporary file) and fill that with
-MS data from two mzML files (from the <em><a href="https://bioconductor.org/packages/3.20/msdata" class="external-link">msdata</a></em>
+MS data from two mzML files (from the <em><a href="https://bioconductor.org/packages/3.21/msdata" class="external-link">msdata</a></em>
 package).</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://rsqlite.r-dbi.org" class="external-link">RSQLite</a></span><span class="op">)</span></span>
@@ -172,7 +172,7 @@ <h2 id="creating-and-using-msbackendsql-sql-databases">Creating and using <code>
 <span><span class="co">## 1862         1          NA         1</span></span>
 <span><span class="co">##  ... 34 more variables/columns.</span></span>
 <span><span class="co">##  Use  'spectraVariables' to list all of them.</span></span>
-<span><span class="co">## Database: /tmp/RtmpWP4Rr5/fileb286077e2da</span></span></code></pre>
+<span><span class="co">## Database: /tmp/Rtmp8LKjpZ/file7725e5d074d</span></span></code></pre>
 <p>As an alternative, the <code>MsBackendOfflineSql</code> backend could
 also be used to interface with MS data in a SQL database. In contrast to
 the <code>MsBackendSql</code>, the <code>MsBackendOfflineSql</code> does
@@ -207,7 +207,7 @@ <h2 id="creating-and-using-msbackendsql-sql-databases">Creating and using <code>
 <span><span class="co">## 1862         1   259.752       931</span></span>
 <span><span class="co">##  ... 34 more variables/columns.</span></span>
 <span><span class="co">## Processing:</span></span>
-<span><span class="co">##  Switch backend from MsBackendSql to MsBackendMemory [Fri Sep 27 05:10:08 2024]</span></span></code></pre>
+<span><span class="co">##  Switch backend from MsBackendSql to MsBackendMemory [Sun Nov 17 16:34:32 2024]</span></span></code></pre>
 <p>With this function it is also possible to change from any backend to
 a <code>MsBackendSql</code> in which case a new database is created and
 all data from the originating backend is stored in this database. To
@@ -241,10 +241,10 @@ <h2 id="creating-and-using-msbackendsql-sql-databases">Creating and using <code>
 <span><span class="co">## 1862         1          NA         1</span></span>
 <span><span class="co">##  ... 34 more variables/columns.</span></span>
 <span><span class="co">##  Use  'spectraVariables' to list all of them.</span></span>
-<span><span class="co">## Database: /tmp/RtmpWP4Rr5/fileb2839a46d9b</span></span>
+<span><span class="co">## Database: /tmp/Rtmp8LKjpZ/file772556f9c57e</span></span>
 <span><span class="co">## Processing:</span></span>
-<span><span class="co">##  Switch backend from MsBackendSql to MsBackendMemory [Fri Sep 27 05:10:08 2024]</span></span>
-<span><span class="co">##  Switch backend from MsBackendMemory to MsBackendOfflineSql [Fri Sep 27 05:10:08 2024]</span></span></code></pre>
+<span><span class="co">##  Switch backend from MsBackendSql to MsBackendMemory [Sun Nov 17 16:34:32 2024]</span></span>
+<span><span class="co">##  Switch backend from MsBackendMemory to MsBackendOfflineSql [Sun Nov 17 16:34:33 2024]</span></span></code></pre>
 <p>Similar to any other <code>Spectra</code> object we can retrieve the
 available <em>spectra variables</em> using the
 <code><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">spectraVariables()</a></code> function.</p>
@@ -310,18 +310,18 @@ <h2 id="creating-and-using-msbackendsql-sql-databases">Creating and using <code>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">msLevel</a></span><span class="op">(</span><span class="va">sps</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">##    user  system elapsed </span></span>
-<span><span class="co">##   0.007   0.001   0.008</span></span></code></pre>
+<span><span class="co">##   0.007   0.000   0.007</span></span></code></pre>
 <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">sps</span><span class="op">$</span><span class="va">msLevel</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">msLevel</a></span><span class="op">(</span><span class="va">sps</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">msLevel</a></span><span class="op">(</span><span class="va">sps</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">##    user  system elapsed </span></span>
-<span><span class="co">##   0.002   0.000   0.002</span></span></code></pre>
-<p>We can also use the <code><a href="https://rdrr.io/pkg/Spectra/man/hidden_aliases.html" class="external-link">reset()</a></code> function to <em>reset</em>
+<span><span class="co">##   0.002   0.000   0.003</span></span></code></pre>
+<p>We can also use the <code><a href="https://rdrr.io/pkg/Spectra/man/addProcessing.html" class="external-link">reset()</a></code> function to <em>reset</em>
 the data to its original state (this will cause any local spectra
 variables to be deleted and the backend to be initialized with the
 original data in the database).</p>
 <div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">sps</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/Spectra/man/hidden_aliases.html" class="external-link">reset</a></span><span class="op">(</span><span class="va">sps</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">sps</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/Spectra/man/addProcessing.html" class="external-link">reset</a></span><span class="op">(</span><span class="va">sps</span><span class="op">)</span></span></code></pre></div>
 <p>To use the <code>MsBackendOfflineSql</code> backend we need to
 provide all information required to connect to the database along with
 the <em>database driver</em> to the <code>Spectra</code> function. Which
@@ -353,7 +353,7 @@ <h2 id="creating-and-using-msbackendsql-sql-databases">Creating and using <code>
 <span><span class="co">## 1862         1          NA         1</span></span>
 <span><span class="co">##  ... 34 more variables/columns.</span></span>
 <span><span class="co">##  Use  'spectraVariables' to list all of them.</span></span>
-<span><span class="co">## Database: /tmp/RtmpWP4Rr5/fileb286077e2da</span></span></code></pre>
+<span><span class="co">## Database: /tmp/Rtmp8LKjpZ/file7725e5d074d</span></span></code></pre>
 <p>This backend provides the exact same functionality than
 <code>MsBackendSql</code> with the difference that the connection to the
 database is opened and closed for each function call. While this leads
@@ -373,8 +373,8 @@ <h2 id="creating-and-using-msbackendsql-sql-databases">Creating and using <code>
 <span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">msLevel</a></span><span class="op">(</span><span class="va">sps</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">msLevel</a></span><span class="op">(</span><span class="va">sps_off</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Unit: milliseconds</span></span>
 <span><span class="co">##              expr      min       lq     mean   median       uq      max neval</span></span>
-<span><span class="co">##      msLevel(sps) 5.332318 5.406762 5.649273 5.476532 5.542425 10.26601   100</span></span>
-<span><span class="co">##  msLevel(sps_off) 6.649957 6.818596 6.973694 6.867898 6.938871 10.00390   100</span></span></code></pre>
+<span><span class="co">##      msLevel(sps) 5.318853 5.582285 5.776706 5.666632 5.802756 10.35720   100</span></span>
+<span><span class="co">##  msLevel(sps_off) 6.942943 7.330998 7.620031 7.530921 7.715440 12.08204   100</span></span></code></pre>
 </div>
 <div class="section level2">
 <h2 id="performance-comparison-with-other-backends">Performance comparison with other backends<a class="anchor" aria-label="anchor" href="#performance-comparison-with-other-backends"></a>
@@ -425,10 +425,10 @@ <h2 id="performance-comparison-with-other-backends">Performance comparison with
 <span>               <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">msLevel</a></span><span class="op">(</span><span class="va">sps_mzr</span><span class="op">)</span>,</span>
 <span>               <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">msLevel</a></span><span class="op">(</span><span class="va">sps_im</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Unit: microseconds</span></span>
-<span><span class="co">##              expr      min        lq       mean    median        uq      max</span></span>
-<span><span class="co">##      msLevel(sps) 5350.232 5537.7015 5771.88027 5626.0110 5741.3965 9305.801</span></span>
-<span><span class="co">##  msLevel(sps_mzr)  367.796  400.6125  432.38209  420.9550  439.0395  650.835</span></span>
-<span><span class="co">##   msLevel(sps_im)   10.830   13.4655   21.04269   20.3735   23.6145   72.585</span></span>
+<span><span class="co">##              expr      min       lq       mean   median        uq      max</span></span>
+<span><span class="co">##      msLevel(sps) 5307.963 5531.631 5855.78739 5777.007 6070.2650 9645.986</span></span>
+<span><span class="co">##  msLevel(sps_mzr)  369.430  391.065  406.52328  405.011  416.6575  642.689</span></span>
+<span><span class="co">##   msLevel(sps_im)   10.861   13.776   22.43835   20.348   27.7165   65.723</span></span>
 <span><span class="co">##  neval</span></span>
 <span><span class="co">##    100</span></span>
 <span><span class="co">##    100</span></span>
@@ -445,13 +445,13 @@ <h2 id="performance-comparison-with-other-backends">Performance comparison with
 <span>               <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/peaksData.html" class="external-link">peaksData</a></span><span class="op">(</span><span class="va">sps_im</span>, BPPARAM <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/BiocParallel/man/SerialParam-class.html" class="external-link">SerialParam</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Unit: microseconds</span></span>
 <span><span class="co">##                                         expr        min         lq       mean</span></span>
-<span><span class="co">##      peaksData(sps, BPPARAM = SerialParam()) 106775.187 120725.956 285957.611</span></span>
-<span><span class="co">##  peaksData(sps_mzr, BPPARAM = SerialParam()) 451588.290 456703.688 751336.931</span></span>
-<span><span class="co">##   peaksData(sps_im, BPPARAM = SerialParam())    357.737    405.517   2317.596</span></span>
-<span><span class="co">##      median          uq        max neval</span></span>
-<span><span class="co">##  350136.025  388083.791  514076.63    10</span></span>
-<span><span class="co">##  770254.801 1077836.403 1114988.63    10</span></span>
-<span><span class="co">##     546.204     653.339   18531.44    10</span></span></code></pre>
+<span><span class="co">##      peaksData(sps, BPPARAM = SerialParam())  99135.484 125869.681 237565.851</span></span>
+<span><span class="co">##  peaksData(sps_mzr, BPPARAM = SerialParam()) 437705.436 455328.668 631429.534</span></span>
+<span><span class="co">##   peaksData(sps_im, BPPARAM = SerialParam())    307.164    348.019   1905.919</span></span>
+<span><span class="co">##       median         uq       max neval</span></span>
+<span><span class="co">##  129195.3065 376300.534  564061.9    10</span></span>
+<span><span class="co">##  480673.1690 708454.956 1184310.8    10</span></span>
+<span><span class="co">##     539.9725    665.401   14498.5    10</span></span></code></pre>
 <p>As expected, the <code>MsBackendMemory</code> has the fasted access
 to the full peaks data. The <code>MsBackendSql</code> outperforms
 however the <code>MsBackendMzR</code> providing faster access to the m/z
@@ -467,28 +467,28 @@ <h2 id="performance-comparison-with-other-backends">Performance comparison with
 <span>               <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/peaksData.html" class="external-link">peaksData</a></span><span class="op">(</span><span class="va">sps_mzr</span>, BPPARAM <span class="op">=</span> <span class="va">m2</span><span class="op">)</span>,</span>
 <span>               <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/peaksData.html" class="external-link">peaksData</a></span><span class="op">(</span><span class="va">sps_im</span>, BPPARAM <span class="op">=</span> <span class="va">m2</span><span class="op">)</span>, times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Unit: microseconds</span></span>
-<span><span class="co">##                              expr        min         lq        mean      median</span></span>
-<span><span class="co">##      peaksData(sps, BPPARAM = m2)  96809.705 106153.578 171793.8454 125550.1305</span></span>
-<span><span class="co">##  peaksData(sps_mzr, BPPARAM = m2) 463529.496 485036.802 675009.7979 649723.4730</span></span>
-<span><span class="co">##   peaksData(sps_im, BPPARAM = m2)    383.796    618.193    605.1018    644.4725</span></span>
+<span><span class="co">##                              expr        min         lq        mean    median</span></span>
+<span><span class="co">##      peaksData(sps, BPPARAM = m2) 103799.987 110091.265 121073.2584 124252.54</span></span>
+<span><span class="co">##  peaksData(sps_mzr, BPPARAM = m2) 446914.127 479684.756 695696.4720 532158.70</span></span>
+<span><span class="co">##   peaksData(sps_im, BPPARAM = m2)    306.402    622.722    607.9765    648.45</span></span>
 <span><span class="co">##          uq         max neval</span></span>
-<span><span class="co">##  133632.325  396552.127    10</span></span>
-<span><span class="co">##  783405.630 1125822.560    10</span></span>
-<span><span class="co">##     674.268     724.341    10</span></span></code></pre>
+<span><span class="co">##  129857.883  133608.220    10</span></span>
+<span><span class="co">##  862147.247 1192024.219    10</span></span>
+<span><span class="co">##     700.147     806.245    10</span></span></code></pre>
 <p>We next compare the performance of subsetting operations.</p>
 <div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">filterRt</a></span><span class="op">(</span><span class="va">sps</span>, rt <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">50</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>               <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">filterRt</a></span><span class="op">(</span><span class="va">sps_mzr</span>, rt <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">50</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>               <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">filterRt</a></span><span class="op">(</span><span class="va">sps_im</span>, rt <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">50</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Unit: microseconds</span></span>
-<span><span class="co">##                                expr      min       lq      mean   median</span></span>
-<span><span class="co">##      filterRt(sps, rt = c(50, 100)) 2685.972 2748.231 2976.2252 2797.785</span></span>
-<span><span class="co">##  filterRt(sps_mzr, rt = c(50, 100)) 2030.728 2141.570 2333.1756 2206.873</span></span>
-<span><span class="co">##   filterRt(sps_im, rt = c(50, 100))  452.784  485.421  522.1169  507.597</span></span>
-<span><span class="co">##         uq       max neval</span></span>
-<span><span class="co">##  2861.4985 17459.073   100</span></span>
-<span><span class="co">##  2421.4225  6680.685   100</span></span>
-<span><span class="co">##   548.1525   895.580   100</span></span></code></pre>
+<span><span class="co">##                                expr      min       lq      mean    median</span></span>
+<span><span class="co">##      filterRt(sps, rt = c(50, 100)) 2622.873 2706.966 3027.5222 2795.5560</span></span>
+<span><span class="co">##  filterRt(sps_mzr, rt = c(50, 100)) 2015.090 2126.502 2345.2143 2251.5955</span></span>
+<span><span class="co">##   filterRt(sps_im, rt = c(50, 100))  441.944  482.270  528.7807  523.4665</span></span>
+<span><span class="co">##        uq       max neval</span></span>
+<span><span class="co">##  2913.697 19829.285   100</span></span>
+<span><span class="co">##  2433.660  7559.725   100</span></span>
+<span><span class="co">##   550.512   901.602   100</span></span></code></pre>
 <p>The two <em>on-disk</em> backends <code>MsBackendSql</code> and
 <code>MsBackendMzR</code> show a comparable performance for this
 operation. This filtering does involves access to a spectra variables
@@ -508,10 +508,10 @@ <h2 id="performance-comparison-with-other-backends">Performance comparison with
 <span>               <span class="va">sps_mzr</span><span class="op">[</span><span class="va">idx</span><span class="op">]</span>,</span>
 <span>               <span class="va">sps_im</span><span class="op">[</span><span class="va">idx</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Unit: microseconds</span></span>
-<span><span class="co">##          expr     min       lq     mean   median       uq     max neval</span></span>
-<span><span class="co">##      sps[idx] 132.798 141.6640 152.3949 150.5610 157.0680 280.623   100</span></span>
-<span><span class="co">##  sps_mzr[idx] 643.571 669.1335 685.4696 678.8715 694.1505 927.961   100</span></span>
-<span><span class="co">##   sps_im[idx] 223.306 234.2920 243.9662 241.7510 250.4520 367.947   100</span></span></code></pre>
+<span><span class="co">##          expr     min       lq     mean   median       uq      max neval</span></span>
+<span><span class="co">##      sps[idx] 131.346 137.7065 149.3402 147.8110 153.1410  275.354   100</span></span>
+<span><span class="co">##  sps_mzr[idx] 633.662 646.4010 671.5505 656.3600 674.0125 1525.096   100</span></span>
+<span><span class="co">##   sps_im[idx] 225.120 231.8025 241.7284 237.3625 245.5230  401.359   100</span></span></code></pre>
 <p>Here the <code>MsBackendSql</code> outperforms the other backends
 because it does not keep any data in memory and hence does not need to
 subset these. The two other backends need to subset the data they keep
@@ -529,14 +529,14 @@ <h2 id="performance-comparison-with-other-backends">Performance comparison with
 <span>               <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/peaksData.html" class="external-link">peaksData</a></span><span class="op">(</span><span class="va">sps_im_10</span><span class="op">)</span>,</span>
 <span>               times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Unit: microseconds</span></span>
-<span><span class="co">##                   expr      min        lq       mean    median        uq</span></span>
-<span><span class="co">##      peaksData(sps_10)  2647.50  2654.273  3291.1344  3614.394  3715.712</span></span>
-<span><span class="co">##  peaksData(sps_mzr_10) 69819.87 72925.655 73515.5042 73877.762 74639.904</span></span>
-<span><span class="co">##   peaksData(sps_im_10)   348.27   406.358   510.9153   447.791   612.092</span></span>
+<span><span class="co">##                   expr       min        lq       mean    median        uq</span></span>
+<span><span class="co">##      peaksData(sps_10)  2624.136  2776.300  3438.1887  3754.535  3959.327</span></span>
+<span><span class="co">##  peaksData(sps_mzr_10) 74668.808 76957.188 77493.6373 77753.818 78581.648</span></span>
+<span><span class="co">##   peaksData(sps_im_10)   359.410   389.236   471.2794   442.415   568.882</span></span>
 <span><span class="co">##        max neval</span></span>
-<span><span class="co">##   3878.386    10</span></span>
-<span><span class="co">##  75518.083    10</span></span>
-<span><span class="co">##    863.561    10</span></span></code></pre>
+<span><span class="co">##   4076.656    10</span></span>
+<span><span class="co">##  78690.992    10</span></span>
+<span><span class="co">##    608.756    10</span></span></code></pre>
 <p>The <code>MsBackendSql</code> outperforms the
 <code>MsBackendMzR</code> while, not unexpectedly, the
 <code>MsBackendMemory</code> provides fasted access.</p>
@@ -607,13 +607,13 @@ <h2 id="session-information">Session information<a class="anchor" aria-label="an
 </h2>
 <div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## R version 4.4.1 (2024-06-14)</span></span>
+<pre><code><span><span class="co">## R Under development (unstable) (2024-11-13 r87330)</span></span>
 <span><span class="co">## Platform: x86_64-pc-linux-gnu</span></span>
-<span><span class="co">## Running under: Ubuntu 22.04.4 LTS</span></span>
+<span><span class="co">## Running under: Ubuntu 24.04.1 LTS</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Matrix products: default</span></span>
 <span><span class="co">## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 </span></span>
-<span><span class="co">## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0</span></span>
+<span><span class="co">## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## locale:</span></span>
 <span><span class="co">##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              </span></span>
@@ -631,29 +631,29 @@ <h2 id="session-information">Session information<a class="anchor" aria-label="an
 <span><span class="co">## [8] base     </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## other attached packages:</span></span>
-<span><span class="co">## [1] microbenchmark_1.5.0 RSQLite_2.3.7        MsBackendSql_1.5.0  </span></span>
-<span><span class="co">## [4] Spectra_1.15.8       ProtGenerics_1.37.1  BiocParallel_1.39.0 </span></span>
-<span><span class="co">## [7] S4Vectors_0.43.2     BiocGenerics_0.51.1  BiocStyle_2.33.1    </span></span>
+<span><span class="co">## [1] microbenchmark_1.5.0 RSQLite_2.3.7        MsBackendSql_1.7.0  </span></span>
+<span><span class="co">## [4] Spectra_1.17.0       BiocParallel_1.41.0  S4Vectors_0.45.2    </span></span>
+<span><span class="co">## [7] BiocGenerics_0.53.3  generics_0.1.3       BiocStyle_2.35.0    </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## loaded via a namespace (and not attached):</span></span>
-<span><span class="co">##  [1] sass_0.4.9             MsCoreUtils_1.17.2     hms_1.1.3             </span></span>
-<span><span class="co">##  [4] digest_0.6.37          evaluate_1.0.0         bookdown_0.40         </span></span>
+<span><span class="co">##  [1] sass_0.4.9             MsCoreUtils_1.19.0     hms_1.1.3             </span></span>
+<span><span class="co">##  [4] digest_0.6.37          evaluate_1.0.1         bookdown_0.41         </span></span>
 <span><span class="co">##  [7] fastmap_1.2.0          blob_1.2.4             jsonlite_1.8.9        </span></span>
-<span><span class="co">## [10] progress_1.2.3         mzR_2.39.0             DBI_1.2.3             </span></span>
-<span><span class="co">## [13] BiocManager_1.30.25    codetools_0.2-20       textshaping_0.4.0     </span></span>
-<span><span class="co">## [16] jquerylib_0.1.4        cli_3.6.3              rlang_1.1.4           </span></span>
-<span><span class="co">## [19] crayon_1.5.3           Biobase_2.65.1         bit64_4.5.2           </span></span>
-<span><span class="co">## [22] cachem_1.1.0           yaml_2.3.10            tools_4.4.1           </span></span>
-<span><span class="co">## [25] parallel_4.4.1         memoise_2.0.1          ncdf4_1.23            </span></span>
-<span><span class="co">## [28] vctrs_0.6.5            R6_2.5.1               lifecycle_1.0.4       </span></span>
-<span><span class="co">## [31] fs_1.6.4               htmlwidgets_1.6.4      IRanges_2.39.2        </span></span>
-<span><span class="co">## [34] bit_4.5.0              clue_0.3-65            MASS_7.3-61           </span></span>
-<span><span class="co">## [37] ragg_1.3.3             cluster_2.1.6          pkgconfig_2.0.3       </span></span>
-<span><span class="co">## [40] desc_1.4.3             pkgdown_2.1.1.9000     bslib_0.8.0           </span></span>
-<span><span class="co">## [43] Rcpp_1.0.13            data.table_1.16.0      systemfonts_1.1.0     </span></span>
-<span><span class="co">## [46] xfun_0.47              knitr_1.48             htmltools_0.5.8.1     </span></span>
-<span><span class="co">## [49] rmarkdown_2.28         compiler_4.4.1         prettyunits_1.2.0     </span></span>
-<span><span class="co">## [52] MetaboCoreUtils_1.13.0</span></span></code></pre>
+<span><span class="co">## [10] ProtGenerics_1.39.0    progress_1.2.3         mzR_2.41.0            </span></span>
+<span><span class="co">## [13] DBI_1.2.3              BiocManager_1.30.25    codetools_0.2-20      </span></span>
+<span><span class="co">## [16] textshaping_0.4.0      jquerylib_0.1.4        cli_3.6.3             </span></span>
+<span><span class="co">## [19] rlang_1.1.4            crayon_1.5.3           Biobase_2.67.0        </span></span>
+<span><span class="co">## [22] bit64_4.5.2            cachem_1.1.0           yaml_2.3.10           </span></span>
+<span><span class="co">## [25] tools_4.5.0            parallel_4.5.0         memoise_2.0.1         </span></span>
+<span><span class="co">## [28] ncdf4_1.23             vctrs_0.6.5            R6_2.5.1              </span></span>
+<span><span class="co">## [31] lifecycle_1.0.4        fs_1.6.5               htmlwidgets_1.6.4     </span></span>
+<span><span class="co">## [34] IRanges_2.41.1         bit_4.5.0              clue_0.3-66           </span></span>
+<span><span class="co">## [37] MASS_7.3-61            ragg_1.3.3             cluster_2.1.6         </span></span>
+<span><span class="co">## [40] pkgconfig_2.0.3        desc_1.4.3             pkgdown_2.1.1.9000    </span></span>
+<span><span class="co">## [43] bslib_0.8.0            Rcpp_1.0.13-1          data.table_1.16.2     </span></span>
+<span><span class="co">## [46] systemfonts_1.1.0      xfun_0.49              knitr_1.49            </span></span>
+<span><span class="co">## [49] htmltools_0.5.8.1      rmarkdown_2.29         compiler_4.5.0        </span></span>
+<span><span class="co">## [52] prettyunits_1.2.0      MetaboCoreUtils_1.15.0</span></span></code></pre>
 </div>
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     </nav></aside>
diff --git a/articles/index.html b/articles/index.html
index 81d443b..085b360 100644
--- a/articles/index.html
+++ b/articles/index.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>Articles • MsBackendSql</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="Articles"><meta property="og:image" content="https://rformassspectrometry.github.io/MsBackendSql/logo.png"></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"><title>Articles • MsBackendSql</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-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/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="Articles"><meta property="og:image" content="https://rformassspectrometry.github.io/MsBackendSql/logo.png"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MsBackendSql</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.0</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">
diff --git a/authors.html b/authors.html
index 175e409..5557e4d 100644
--- a/authors.html
+++ b/authors.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>Authors and Citation • MsBackendSql</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="Authors and Citation"><meta property="og:image" content="https://rformassspectrometry.github.io/MsBackendSql/logo.png"></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"><title>Authors and Citation • MsBackendSql</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-6.5.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.5.2/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="Authors and Citation"><meta property="og:image" content="https://rformassspectrometry.github.io/MsBackendSql/logo.png"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">MsBackendSql</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.0</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">
@@ -54,13 +54,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Rainer J (2024).
 <em>MsBackendSql: SQL-based Mass Spectrometry Data Backend</em>.
-R package version 1.5.0, <a href="https://github.com/RforMassSpectrometry/MsBackendSql" class="external-link">https://github.com/RforMassSpectrometry/MsBackendSql</a>.
+R package version 1.7.0, <a href="https://github.com/RforMassSpectrometry/MsBackendSql" class="external-link">https://github.com/RforMassSpectrometry/MsBackendSql</a>.
 </p>
       <pre>@Manual{,
   title = {MsBackendSql: SQL-based Mass Spectrometry Data Backend},
   author = {Johannes Rainer},
   year = {2024},
-  note = {R package version 1.5.0},
+  note = {R package version 1.7.0},
   url = {https://github.com/RforMassSpectrometry/MsBackendSql},
 }</pre>
     </div>
diff --git a/deps/data-deps.txt b/deps/data-deps.txt
index 8aa49e2..ca4dfd9 100644
--- a/deps/data-deps.txt
+++ b/deps/data-deps.txt
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-<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
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diff --git a/deps/font-awesome-6.4.2/css/all.min.css b/deps/font-awesome-6.4.2/css/all.min.css
deleted file mode 100644
index 6604a06..0000000
--- a/deps/font-awesome-6.4.2/css/all.min.css
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400 1em/1 "Font Awesome 6 Free"}@font-face{font-family:"Font Awesome 6 Free";font-style:normal;font-weight:400;font-display:block;src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }.fa-regular,.far{font-weight:400}:host,:root{--fa-style-family-classic:"Font Awesome 6 Free";--fa-font-solid:normal 900 1em/1 "Font Awesome 6 Free"}@font-face{font-family:"Font Awesome 6 Free";font-style:normal;font-weight:900;font-display:block;src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }.fa-solid,.fas{font-weight:900}@font-face{font-family:"Font Awesome 5 Brands";font-display:block;font-weight:400;src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }@font-face{font-family:"Font Awesome 5 Free";font-display:block;font-weight:900;src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }@font-face{font-family:"Font Awesome 5 Free";font-display:block;font-weight:400;src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }@font-face{font-family:"FontAwesome";font-display:block;src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }@font-face{font-family:"FontAwesome";font-display:block;src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }@font-face{font-family:"FontAwesome";font-display:block;src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }@font-face{font-family:"FontAwesome";font-display:block;src: url("../webfonts/fa-v4compatibility.woff2") format("woff2"), url("../webfonts/fa-v4compatibility.ttf") format("truetype"); }
\ No newline at end of file
diff --git a/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf b/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf
deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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diff --git a/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf b/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf
deleted file mode 100644
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deleted file mode 100644
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diff --git a/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf b/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf
deleted file mode 100644
index ba6cb25..0000000
Binary files a/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf and /dev/null differ
diff --git a/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2 b/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2
deleted file mode 100644
index 23b1c47..0000000
Binary files a/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2 and /dev/null differ
diff --git a/deps/font-awesome-6.4.2/css/all.css b/deps/font-awesome-6.5.2/css/all.css
similarity index 99%
rename from deps/font-awesome-6.4.2/css/all.css
rename to deps/font-awesome-6.5.2/css/all.css
index bdb6e3a..151dd57 100644
--- a/deps/font-awesome-6.4.2/css/all.css
+++ b/deps/font-awesome-6.5.2/css/all.css
@@ -1,7 +1,7 @@
 /*!
- * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
  * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
- * Copyright 2023 Fonticons, Inc.
+ * Copyright 2024 Fonticons, Inc.
  */
 .fa {
   font-family: var(--fa-style-family, "Font Awesome 6 Free");
@@ -463,8 +463,8 @@
           transform: scale(-1, -1); }
 
 .fa-rotate-by {
-  -webkit-transform: rotate(var(--fa-rotate-angle, none));
-          transform: rotate(var(--fa-rotate-angle, none)); }
+  -webkit-transform: rotate(var(--fa-rotate-angle, 0));
+          transform: rotate(var(--fa-rotate-angle, 0)); }
 
 .fa-stack {
   display: inline-block;
@@ -2768,6 +2768,9 @@ readers do not read off random characters that represent icons */
 .fa-italic::before {
   content: "\f033"; }
 
+.fa-table-cells-column-lock::before {
+  content: "\e678"; }
+
 .fa-church::before {
   content: "\f51d"; }
 
@@ -4940,6 +4943,9 @@ readers do not read off random characters that represent icons */
 .fa-font::before {
   content: "\f031"; }
 
+.fa-table-cells-row-lock::before {
+  content: "\e67a"; }
+
 .fa-rupiah-sign::before {
   content: "\e23d"; }
 
@@ -5969,9 +5975,6 @@ readers do not read off random characters that represent icons */
 .fa-share::before {
   content: "\f064"; }
 
-.fa-arrow-turn-right::before {
-  content: "\f064"; }
-
 .fa-mail-forward::before {
   content: "\f064"; }
 
@@ -6421,6 +6424,9 @@ readers do not read off random characters that represent icons */
 .fa-ups:before {
   content: "\f7e0"; }
 
+.fa-pixiv:before {
+  content: "\e640"; }
+
 .fa-wpexplorer:before {
   content: "\f2de"; }
 
@@ -6481,6 +6487,9 @@ readers do not read off random characters that represent icons */
 .fa-drupal:before {
   content: "\f1a9"; }
 
+.fa-jxl:before {
+  content: "\e67b"; }
+
 .fa-hire-a-helper:before {
   content: "\f3b0"; }
 
@@ -6526,6 +6535,9 @@ readers do not read off random characters that represent icons */
 .fa-deskpro:before {
   content: "\f38f"; }
 
+.fa-brave:before {
+  content: "\e63c"; }
+
 .fa-sistrix:before {
   content: "\f3ee"; }
 
@@ -6694,6 +6706,9 @@ readers do not read off random characters that represent icons */
 .fa-cloudsmith:before {
   content: "\f384"; }
 
+.fa-opensuse:before {
+  content: "\e62b"; }
+
 .fa-pied-piper-alt:before {
   content: "\f1a8"; }
 
@@ -6778,6 +6793,9 @@ readers do not read off random characters that represent icons */
 .fa-kickstarter:before {
   content: "\f3bb"; }
 
+.fa-square-kickstarter:before {
+  content: "\f3bb"; }
+
 .fa-grav:before {
   content: "\f2d6"; }
 
@@ -6838,6 +6856,9 @@ readers do not read off random characters that represent icons */
 .fa-bluetooth-b:before {
   content: "\f294"; }
 
+.fa-square-letterboxd:before {
+  content: "\e62e"; }
+
 .fa-sticker-mule:before {
   content: "\f3f7"; }
 
@@ -6871,6 +6892,9 @@ readers do not read off random characters that represent icons */
 .fa-confluence:before {
   content: "\f78d"; }
 
+.fa-shoelace:before {
+  content: "\e60c"; }
+
 .fa-mdb:before {
   content: "\f8ca"; }
 
@@ -6994,6 +7018,9 @@ readers do not read off random characters that represent icons */
 .fa-envira:before {
   content: "\f299"; }
 
+.fa-google-scholar:before {
+  content: "\e63b"; }
+
 .fa-square-gitlab:before {
   content: "\e5ae"; }
 
@@ -7126,6 +7153,9 @@ readers do not read off random characters that represent icons */
 .fa-vine:before {
   content: "\f1ca"; }
 
+.fa-signal-messenger:before {
+  content: "\e663"; }
+
 .fa-paypal:before {
   content: "\f1ed"; }
 
@@ -7159,6 +7189,9 @@ readers do not read off random characters that represent icons */
 .fa-nfc-symbol:before {
   content: "\e531"; }
 
+.fa-mintbit:before {
+  content: "\e62f"; }
+
 .fa-ethereum:before {
   content: "\f42e"; }
 
@@ -7183,6 +7216,9 @@ readers do not read off random characters that represent icons */
 .fa-bimobject:before {
   content: "\f378"; }
 
+.fa-brave-reverse:before {
+  content: "\e63d"; }
+
 .fa-facebook-f:before {
   content: "\f39e"; }
 
@@ -7192,6 +7228,9 @@ readers do not read off random characters that represent icons */
 .fa-google-plus-square:before {
   content: "\f0d4"; }
 
+.fa-web-awesome:before {
+  content: "\e682"; }
+
 .fa-mandalorian:before {
   content: "\f50f"; }
 
@@ -7285,6 +7324,9 @@ readers do not read off random characters that represent icons */
 .fa-tencent-weibo:before {
   content: "\f1d5"; }
 
+.fa-letterboxd:before {
+  content: "\e62d"; }
+
 .fa-symfony:before {
   content: "\f83d"; }
 
@@ -7351,6 +7393,9 @@ readers do not read off random characters that represent icons */
 .fa-xbox:before {
   content: "\f412"; }
 
+.fa-square-web-awesome-stroke:before {
+  content: "\e684"; }
+
 .fa-searchengin:before {
   content: "\f3eb"; }
 
@@ -7423,6 +7468,9 @@ readers do not read off random characters that represent icons */
 .fa-cmplid:before {
   content: "\e360"; }
 
+.fa-upwork:before {
+  content: "\e641"; }
+
 .fa-facebook:before {
   content: "\f09a"; }
 
@@ -7456,6 +7504,9 @@ readers do not read off random characters that represent icons */
 .fa-whatsapp:before {
   content: "\f232"; }
 
+.fa-square-upwork:before {
+  content: "\e67c"; }
+
 .fa-slideshare:before {
   content: "\f1e7"; }
 
@@ -7534,6 +7585,9 @@ readers do not read off random characters that represent icons */
 .fa-sellsy:before {
   content: "\f213"; }
 
+.fa-square-web-awesome:before {
+  content: "\e683"; }
+
 .fa-sass:before {
   content: "\f41e"; }
 
@@ -7570,6 +7624,9 @@ readers do not read off random characters that represent icons */
 .fa-waze:before {
   content: "\f83f"; }
 
+.fa-bluesky:before {
+  content: "\e671"; }
+
 .fa-cc-jcb:before {
   content: "\f24b"; }
 
@@ -7597,6 +7654,9 @@ readers do not read off random characters that represent icons */
 .fa-supple:before {
   content: "\f3f9"; }
 
+.fa-webflow:before {
+  content: "\e65c"; }
+
 .fa-rebel:before {
   content: "\f1d0"; }
 
diff --git a/deps/font-awesome-6.5.2/css/all.min.css b/deps/font-awesome-6.5.2/css/all.min.css
new file mode 100644
index 0000000..269bcee
--- /dev/null
+++ b/deps/font-awesome-6.5.2/css/all.min.css
@@ -0,0 +1,9 @@
+/*!
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2024 Fonticons, Inc.
+ */
+.fa{font-family:var(--fa-style-family,"Font Awesome 6 Free");font-weight:var(--fa-style,900)}.fa,.fa-brands,.fa-classic,.fa-regular,.fa-sharp,.fa-solid,.fab,.far,.fas{-moz-osx-font-smoothing:grayscale;-webkit-font-smoothing:antialiased;display:var(--fa-display,inline-block);font-style:normal;font-variant:normal;line-height:1;text-rendering:auto}.fa-classic,.fa-regular,.fa-solid,.far,.fas{font-family:"Font Awesome 6 Free"}.fa-brands,.fab{font-family:"Font Awesome 6 Brands"}.fa-1x{font-size:1em}.fa-2x{font-size:2em}.fa-3x{font-size:3em}.fa-4x{font-size:4em}.fa-5x{font-size:5em}.fa-6x{font-size:6em}.fa-7x{font-size:7em}.fa-8x{font-size:8em}.fa-9x{font-size:9em}.fa-10x{font-size:10em}.fa-2xs{font-size:.625em;line-height:.1em;vertical-align:.225em}.fa-xs{font-size:.75em;line-height:.08333em;vertical-align:.125em}.fa-sm{font-size:.875em;line-height:.07143em;vertical-align:.05357em}.fa-lg{font-size:1.25em;line-height:.05em;vertical-align:-.075em}.fa-xl{font-size:1.5em;line-height:.04167em;vertical-align:-.125em}.fa-2xl{font-size:2em;line-height:.03125em;vertical-align:-.1875em}.fa-fw{text-align:center;width:1.25em}.fa-ul{list-style-type:none;margin-left:var(--fa-li-margin,2.5em);padding-left:0}.fa-ul>li{position:relative}.fa-li{left:calc(var(--fa-li-width, 2em)*-1);position:absolute;text-align:center;width:var(--fa-li-width,2em);line-height:inherit}.fa-border{border-radius:var(--fa-border-radius,.1em);border:var(--fa-border-width,.08em) var(--fa-border-style,solid) var(--fa-border-color,#eee);padding:var(--fa-border-padding,.2em .25em .15em)}.fa-pull-left{float:left;margin-right:var(--fa-pull-margin,.3em)}.fa-pull-right{float:right;margin-left:var(--fa-pull-margin,.3em)}.fa-beat{-webkit-animation-name:fa-beat;animation-name:fa-beat;-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,ease-in-out);animation-timing-function:var(--fa-animation-timing,ease-in-out)}.fa-bounce{-webkit-animation-name:fa-bounce;animation-name:fa-bounce;-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,cubic-bezier(.28,.84,.42,1));animation-timing-function:var(--fa-animation-timing,cubic-bezier(.28,.84,.42,1))}.fa-fade{-webkit-animation-name:fa-fade;animation-name:fa-fade;-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.6,1));animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.6,1))}.fa-beat-fade,.fa-fade{-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s)}.fa-beat-fade{-webkit-animation-name:fa-beat-fade;animation-name:fa-beat-fade;-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.6,1));animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.6,1))}.fa-flip{-webkit-animation-name:fa-flip;animation-name:fa-flip;-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,ease-in-out);animation-timing-function:var(--fa-animation-timing,ease-in-out)}.fa-shake{-webkit-animation-name:fa-shake;animation-name:fa-shake;-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,linear);animation-timing-function:var(--fa-animation-timing,linear)}.fa-shake,.fa-spin{-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal)}.fa-spin{-webkit-animation-name:fa-spin;animation-name:fa-spin;-webkit-animation-duration:var(--fa-animation-duration,2s);animation-duration:var(--fa-animation-duration,2s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,linear);animation-timing-function:var(--fa-animation-timing,linear)}.fa-spin-reverse{--fa-animation-direction:reverse}.fa-pulse,.fa-spin-pulse{-webkit-animation-name:fa-spin;animation-name:fa-spin;-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,steps(8));animation-timing-function:var(--fa-animation-timing,steps(8))}@media (prefers-reduced-motion:reduce){.fa-beat,.fa-beat-fade,.fa-bounce,.fa-fade,.fa-flip,.fa-pulse,.fa-shake,.fa-spin,.fa-spin-pulse{-webkit-animation-delay:-1ms;animation-delay:-1ms;-webkit-animation-duration:1ms;animation-duration:1ms;-webkit-animation-iteration-count:1;animation-iteration-count:1;-webkit-transition-delay:0s;transition-delay:0s;-webkit-transition-duration:0s;transition-duration:0s}}@-webkit-keyframes fa-beat{0%,90%{-webkit-transform:scale(1);transform:scale(1)}45%{-webkit-transform:scale(var(--fa-beat-scale,1.25));transform:scale(var(--fa-beat-scale,1.25))}}@keyframes fa-beat{0%,90%{-webkit-transform:scale(1);transform:scale(1)}45%{-webkit-transform:scale(var(--fa-beat-scale,1.25));transform:scale(var(--fa-beat-scale,1.25))}}@-webkit-keyframes fa-bounce{0%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}10%{-webkit-transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0);transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0)}30%{-webkit-transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em));transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em))}50%{-webkit-transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0);transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0)}57%{-webkit-transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em));transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em))}64%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}to{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}}@keyframes fa-bounce{0%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}10%{-webkit-transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0);transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0)}30%{-webkit-transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em));transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em))}50%{-webkit-transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0);transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0)}57%{-webkit-transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em));transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em))}64%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}to{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}}@-webkit-keyframes fa-fade{50%{opacity:var(--fa-fade-opacity,.4)}}@keyframes fa-fade{50%{opacity:var(--fa-fade-opacity,.4)}}@-webkit-keyframes fa-beat-fade{0%,to{opacity:var(--fa-beat-fade-opacity,.4);-webkit-transform:scale(1);transform:scale(1)}50%{opacity:1;-webkit-transform:scale(var(--fa-beat-fade-scale,1.125));transform:scale(var(--fa-beat-fade-scale,1.125))}}@keyframes fa-beat-fade{0%,to{opacity:var(--fa-beat-fade-opacity,.4);-webkit-transform:scale(1);transform:scale(1)}50%{opacity:1;-webkit-transform:scale(var(--fa-beat-fade-scale,1.125));transform:scale(var(--fa-beat-fade-scale,1.125))}}@-webkit-keyframes fa-flip{50%{-webkit-transform:rotate3d(var(--fa-flip-x,0),var(--fa-flip-y,1),var(--fa-flip-z,0),var(--fa-flip-angle,-180deg));transform:rotate3d(var(--fa-flip-x,0),var(--fa-flip-y,1),var(--fa-flip-z,0),var(--fa-flip-angle,-180deg))}}@keyframes fa-flip{50%{-webkit-transform:rotate3d(var(--fa-flip-x,0),var(--fa-flip-y,1),var(--fa-flip-z,0),var(--fa-flip-angle,-180deg));transform:rotate3d(var(--fa-flip-x,0),var(--fa-flip-y,1),var(--fa-flip-z,0),var(--fa-flip-angle,-180deg))}}@-webkit-keyframes fa-shake{0%{-webkit-transform:rotate(-15deg);transform:rotate(-15deg)}4%{-webkit-transform:rotate(15deg);transform:rotate(15deg)}8%,24%{-webkit-transform:rotate(-18deg);transform:rotate(-18deg)}12%,28%{-webkit-transform:rotate(18deg);transform:rotate(18deg)}16%{-webkit-transform:rotate(-22deg);transform:rotate(-22deg)}20%{-webkit-transform:rotate(22deg);transform:rotate(22deg)}32%{-webkit-transform:rotate(-12deg);transform:rotate(-12deg)}36%{-webkit-transform:rotate(12deg);transform:rotate(12deg)}40%,to{-webkit-transform:rotate(0deg);transform:rotate(0deg)}}@keyframes fa-shake{0%{-webkit-transform:rotate(-15deg);transform:rotate(-15deg)}4%{-webkit-transform:rotate(15deg);transform:rotate(15deg)}8%,24%{-webkit-transform:rotate(-18deg);transform:rotate(-18deg)}12%,28%{-webkit-transform:rotate(18deg);transform:rotate(18deg)}16%{-webkit-transform:rotate(-22deg);transform:rotate(-22deg)}20%{-webkit-transform:rotate(22deg);transform:rotate(22deg)}32%{-webkit-transform:rotate(-12deg);transform:rotate(-12deg)}36%{-webkit-transform:rotate(12deg);transform:rotate(12deg)}40%,to{-webkit-transform:rotate(0deg);transform:rotate(0deg)}}@-webkit-keyframes fa-spin{0%{-webkit-transform:rotate(0deg);transform:rotate(0deg)}to{-webkit-transform:rotate(1turn);transform:rotate(1turn)}}@keyframes 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+
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diff --git a/deps/font-awesome-6.4.2/css/v4-shims.css b/deps/font-awesome-6.5.2/css/v4-shims.css
similarity index 99%
rename from deps/font-awesome-6.4.2/css/v4-shims.css
rename to deps/font-awesome-6.5.2/css/v4-shims.css
index a85953d..ea60ea4 100644
--- a/deps/font-awesome-6.4.2/css/v4-shims.css
+++ b/deps/font-awesome-6.5.2/css/v4-shims.css
@@ -1,7 +1,7 @@
 /*!
- * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
  * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
- * Copyright 2023 Fonticons, Inc.
+ * Copyright 2024 Fonticons, Inc.
  */
 .fa.fa-glass:before {
   content: "\f000"; }
diff --git a/deps/font-awesome-6.4.2/css/v4-shims.min.css b/deps/font-awesome-6.5.2/css/v4-shims.min.css
similarity index 99%
rename from deps/font-awesome-6.4.2/css/v4-shims.min.css
rename to deps/font-awesome-6.5.2/css/v4-shims.min.css
index 64e4e8d..09baf5f 100644
--- a/deps/font-awesome-6.4.2/css/v4-shims.min.css
+++ b/deps/font-awesome-6.5.2/css/v4-shims.min.css
@@ -1,6 +1,6 @@
 /*!
- * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
  * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
- * Copyright 2023 Fonticons, Inc.
+ * Copyright 2024 Fonticons, Inc.
  */
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diff --git a/index.html b/index.html
index c3ae02d..c54df9a 100644
--- a/index.html
+++ b/index.html
@@ -8,8 +8,8 @@
 <title>SQL-based Mass Spectrometry Data Backend • MsBackendSql</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/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
+<link href="deps/font-awesome-6.5.2/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="SQL-based Mass Spectrometry Data Backend">
 <meta name="description" content="SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.">
 <meta property="og:description" content="SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.">
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="index.html">MsBackendSql</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.0</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">
diff --git a/news/index.html b/news/index.html
index 75054b9..5a3a76e 100644
--- a/news/index.html
+++ b/news/index.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>Changelog • MsBackendSql</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="Changelog"><meta property="og:image" content="https://rformassspectrometry.github.io/MsBackendSql/logo.png"></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"><title>Changelog • MsBackendSql</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-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/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="Changelog"><meta property="og:image" content="https://rformassspectrometry.github.io/MsBackendSql/logo.png"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MsBackendSql</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.0</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">
@@ -32,6 +32,13 @@
       <small>Source: <a href="https://github.com/RforMassSpectrometry/MsBackendSql/blob/main/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="1.5" id="msbackendsql-15">MsBackendSql 1.5<a class="anchor" aria-label="anchor" href="#msbackendsql-15"></a></h2>
+<div class="section level3">
+<h3 id="changes-in-1-5">Changes in 1.5.1<a class="anchor" aria-label="anchor" href="#changes-in-1-5"></a></h3>
+<ul><li>Implement the new <code><a href="https://rdrr.io/pkg/Spectra/man/MsBackend.html" class="external-link">extractByIndex()</a></code> methods.</li>
+</ul></div>
+</div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.3" id="msbackendsql-13">MsBackendSql 1.3<a class="anchor" aria-label="anchor" href="#msbackendsql-13"></a></h2>
 <div class="section level3">
diff --git a/pkgdown.yml b/pkgdown.yml
index 4a3098a..c8ecb37 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,9 +1,9 @@
-pandoc: '3.3'
+pandoc: '3.5'
 pkgdown: 2.1.1.9000
-pkgdown_sha: 0a18bc718640aee7160a0ebbcdef5ecaae2ac4a4
+pkgdown_sha: 7645a47b08827c8ff6029c8afd09d9b13674ade5
 articles:
   MsBackendSql: MsBackendSql.html
-last_built: 2024-09-27T05:09Z
+last_built: 2024-11-17T16:34Z
 urls:
   reference: https://rformassspectrometry.github.io/MsBackendSql/reference
   article: https://rformassspectrometry.github.io/MsBackendSql/articles
diff --git a/reference/MsBackendOfflineSql.html b/reference/MsBackendOfflineSql.html
index 48873d7..1c63902 100644
--- a/reference/MsBackendOfflineSql.html
+++ b/reference/MsBackendOfflineSql.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>SQL-based MS backend without active database connection — MsBackendOfflineSql • MsBackendSql</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="SQL-based MS backend without active database connection — MsBackendOfflineSql"><meta name="description" content="The MsBackendOfflineSql backend extends the MsBackendSql() backend
+<!-- 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>SQL-based MS backend without active database connection — MsBackendOfflineSql • MsBackendSql</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-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/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="SQL-based MS backend without active database connection — MsBackendOfflineSql"><meta name="description" content="The MsBackendOfflineSql backend extends the MsBackendSql() backend
 directly and inherits thus all of its functions as well as properties.
 The only difference between the two backend is that MsBackendSql keeps
 an active connection to the SQL database inside the object while the
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MsBackendSql</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.0</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">
diff --git a/reference/MsBackendSql.html b/reference/MsBackendSql.html
index 7a3461c..6f80423 100644
--- a/reference/MsBackendSql.html
+++ b/reference/MsBackendSql.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>Spectra MS backend storing data in a SQL database — MsBackendSql • MsBackendSql</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="Spectra MS backend storing data in a SQL database — MsBackendSql"><meta name="description" content="The MsBackendSql is an implementation for the MsBackend() class for
+<!-- 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>Spectra MS backend storing data in a SQL database — MsBackendSql • MsBackendSql</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-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/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="Spectra MS backend storing data in a SQL database — MsBackendSql"><meta name="description" content="The MsBackendSql is an implementation for the MsBackend() class for
 Spectra() objects which stores and retrieves MS data from a SQL database.
 New databases can be created from raw MS data files using
 createMsBackendSqlDatabase()."><meta property="og:description" content="The MsBackendSql is an implementation for the MsBackend() class for
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MsBackendSql</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.0</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">
@@ -72,6 +72,9 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span><span class="co"># S4 method for class 'MsBackendSql'</span></span>
 <span><span class="va">x</span><span class="op">[</span><span class="va">i</span>, <span class="va">j</span>, <span class="va">...</span>, drop <span class="op">=</span> <span class="cn">FALSE</span><span class="op">]</span></span>
 <span></span>
+<span><span class="co"># S4 method for class 'MsBackendSql,ANY'</span></span>
+<span><span class="fu"><a href="https://rdrr.io/pkg/Spectra/man/MsBackend.html" class="external-link">extractByIndex</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">i</span><span class="op">)</span></span>
+<span></span>
 <span><span class="co"># S4 method for class 'MsBackendSql'</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/peaksData.html" class="external-link">peaksData</a></span><span class="op">(</span><span class="va">object</span>, columns <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">"mz"</span>, <span class="st">"intensity"</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
@@ -91,7 +94,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">spectraData</a></span><span class="op">(</span><span class="va">object</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">spectraVariables</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S4 method for class 'MsBackendSql'</span></span>
-<span><span class="fu"><a href="https://rdrr.io/pkg/Spectra/man/hidden_aliases.html" class="external-link">reset</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/pkg/Spectra/man/addProcessing.html" class="external-link">reset</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S4 method for class 'MsBackendSql'</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">spectraNames</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
@@ -118,10 +121,10 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">uniqueMsLevels</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S4 method for class 'MsBackendSql'</span></span>
-<span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/backendInitialize.html" class="external-link">backendMerge</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">backendMerge</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S4 method for class 'MsBackendSql'</span></span>
-<span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">precScanNum</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
+<span><span class="fu">precScanNum</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S4 method for class 'MsBackendSql'</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">centroided</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
@@ -413,17 +416,17 @@ <h2 id="subsetting-merging-and-filtering-data">Subsetting, merging and filtering
 
 
 
-<p><code>MsBackendSql</code> objects can be subsetted using the <code>[</code> function. Internally,
-this will simply subset the <code>integer</code> vector of the primary keys and
-eventually cached data. The original data in the database <strong>is not</strong>
-affected by any subsetting operation. Any subsetting operation can be
-<em>undone</em> by resetting the object with the <code><a href="https://rdrr.io/pkg/Spectra/man/hidden_aliases.html" class="external-link">reset()</a></code> function. Subsetting
-in arbitrary order as well as index replication is supported.</p>
+<p><code>MsBackendSql</code> objects can be subsetted using the <code>[</code> or <code><a href="https://rdrr.io/pkg/Spectra/man/MsBackend.html" class="external-link">extractByIndex()</a></code>
+functions. Internally, this will simply subset the <code>integer</code> vector of the
+primary keys and eventually cached data. The original data in the database
+<strong>is not</strong> affected by any subsetting operation. Any subsetting operation
+can be <em>undone</em> by resetting the object with the <code><a href="https://rdrr.io/pkg/Spectra/man/addProcessing.html" class="external-link">reset()</a></code> function.
+Subsetting in arbitrary order as well as index replication is supported.</p>
 <p>Multiple <code>MsBackendSql</code> objects can also be merged (combined) with the
-<code><a href="https://rdrr.io/pkg/ProtGenerics/man/backendInitialize.html" class="external-link">backendMerge()</a></code> function. Note that this requires that all <code>MsBackendSql</code>
+<code>backendMerge()</code> function. Note that this requires that all <code>MsBackendSql</code>
 objects are connected to the <strong>same</strong> database. This function is thus
 mostly used for combining <code>MsBackendSql</code> objects that were previously
-splitted using e.g. <code><a href="https://rdrr.io/pkg/S4Vectors/man/splitAsList.html" class="external-link">split()</a></code>.</p>
+splitted using e.g. <code><a href="https://rdrr.io/r/base/split.html" class="external-link">split()</a></code>.</p>
 <p>In addition, <code>MsBackendSql</code> supports all other filtering methods available
 through <code><a href="https://rdrr.io/pkg/Spectra/man/MsBackendCached.html" class="external-link">MsBackendCached()</a></code>. Implementation of filter functions optimized
 for <code>MsBackendSql</code> objects are:</p><ul><li><p><code><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">filterDataOrigin()</a></code>: filter the object retaining spectra with <code>dataOrigin</code>
@@ -469,7 +472,7 @@ <h2 id="accessing-and-modifying-data">Accessing and <em>modifying</em> data<a cl
 <code>columns</code>.</p></li>
 <li><p><code><a href="https://rdrr.io/pkg/ProtGenerics/man/peaksData.html" class="external-link">peaksVariables()</a></code>: returns a <code>character</code> with the available peak
 variables, i.e. columns that could be queried with <code><a href="https://rdrr.io/pkg/ProtGenerics/man/peaksData.html" class="external-link">peaksData()</a></code>.</p></li>
-<li><p><code><a href="https://rdrr.io/pkg/Spectra/man/hidden_aliases.html" class="external-link">reset()</a></code>: <em>restores</em> an <code>MsBackendSql</code> by re-initializing it with the
+<li><p><code><a href="https://rdrr.io/pkg/Spectra/man/addProcessing.html" class="external-link">reset()</a></code>: <em>restores</em> an <code>MsBackendSql</code> by re-initializing it with the
 data from the database. Any subsetting or cached spectra variables will
 be lost.</p></li>
 <li><p><code><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">spectraData()</a></code>: gets general spectrum metadata. <code><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">spectraData()</a></code> returns
@@ -557,7 +560,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> 198         1          NA         1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ... 34 more variables/columns.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Use  'spectraVariables' to list all of them.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Database: /tmp/RtmpqLniVu/filea684cdb5a7b</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Database: /tmp/RtmpjVGmuK/file76664c5f5a0f</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## Original data source</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">be</span><span class="op">$</span><span class="va">dataOrigin</span><span class="op">)</span></span></span>
@@ -570,9 +573,9 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## Data storage</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">dataStorage</a></span><span class="op">(</span><span class="va">be</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "/tmp/RtmpqLniVu/filea684cdb5a7b" "/tmp/RtmpqLniVu/filea684cdb5a7b"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [3] "/tmp/RtmpqLniVu/filea684cdb5a7b" "/tmp/RtmpqLniVu/filea684cdb5a7b"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "/tmp/RtmpqLniVu/filea684cdb5a7b" "/tmp/RtmpqLniVu/filea684cdb5a7b"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "/tmp/RtmpjVGmuK/file76664c5f5a0f" "/tmp/RtmpjVGmuK/file76664c5f5a0f"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [3] "/tmp/RtmpjVGmuK/file76664c5f5a0f" "/tmp/RtmpjVGmuK/file76664c5f5a0f"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "/tmp/RtmpjVGmuK/file76664c5f5a0f" "/tmp/RtmpjVGmuK/file76664c5f5a0f"</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## Access all spectra data</span></span></span>
 <span class="r-in"><span><span class="va">spd</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/ProtGenerics/man/protgenerics.html" class="external-link">spectraData</a></span><span class="op">(</span><span class="va">be</span><span class="op">)</span></span></span>
@@ -593,17 +596,17 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> 198         1   66.7818            198       198    111.044,112.024,112.518,...</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>           intensity            dataStorage             dataOrigin centroided</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       &lt;NumericList&gt;            &lt;character&gt;            &lt;character&gt;  &lt;logical&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1      23,35,50,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    35, 24,140,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3    28,179,350,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4    25, 28,131,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5      26,30,25,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1      23,35,50,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    35, 24,140,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3    28,179,350,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4    25, 28,131,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5      26,30,25,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ...             ...                    ...                    ...        ...</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 194    34,24,86,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 195  24, 22,198,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 196    29,22,98,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 197  31,124,189,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 198    67,84,22,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 194    34,24,86,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 195  24, 22,198,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 196    29,22,98,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 197  31,124,189,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 198    67,84,22,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      smoothed  polarity precScanNum precursorMz precursorIntensity</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     &lt;logical&gt; &lt;integer&gt;   &lt;integer&gt;   &lt;numeric&gt;          &lt;numeric&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1          NA         1          NA          NA                 NA</span>
@@ -748,7 +751,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> 6         1          NA         1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ... 34 more variables/columns.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Use  'spectraVariables' to list all of them.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Database: /tmp/RtmpqLniVu/filea684cdb5a7b</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Database: /tmp/RtmpjVGmuK/file76664c5f5a0f</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## The internal spectrum IDs (primary keys from the database)</span></span></span>
 <span class="r-in"><span><span class="va">be_sub</span><span class="op">$</span><span class="va">spectrum_id_</span></span></span>
diff --git a/reference/extractByIndex,MsBackendSql,ANY-method.html b/reference/extractByIndex,MsBackendSql,ANY-method.html
new file mode 100644
index 0000000..75dc4a5
--- /dev/null
+++ b/reference/extractByIndex,MsBackendSql,ANY-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html">
+  </head>
+</html>
+
diff --git a/reference/index.html b/reference/index.html
index 3d98d34..703fc09 100644
--- a/reference/index.html
+++ b/reference/index.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>Package index • MsBackendSql</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="Package index"><meta property="og:image" content="https://rformassspectrometry.github.io/MsBackendSql/logo.png"></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"><title>Package index • MsBackendSql</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-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/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="Package index"><meta property="og:image" content="https://rformassspectrometry.github.io/MsBackendSql/logo.png"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MsBackendSql</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.0</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">
@@ -50,7 +50,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>SQL-based MS backend without active database connection</dd>
       </dl><dl><dt>
 
-          <code><a href="MsBackendSql.html">MsBackendSql()</a></code> <code><a href="MsBackendSql.html">createMsBackendSqlDatabase()</a></code> <code><a href="MsBackendSql.html">show(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">backendInitialize(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">dataStorage(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`[`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">peaksData(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">peaksVariables(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`intensity&lt;-`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`mz&lt;-`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`$&lt;-`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">spectraData(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">reset(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">spectraNames(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`spectraNames&lt;-`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterMsLevel(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterRt(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterDataOrigin(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterPrecursorMzRange(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterPrecursorMzValues(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">uniqueMsLevels(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">backendMerge(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">precScanNum(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">centroided(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">smoothed(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">tic(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">supportsSetBackend(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">backendBpparam(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">dbconn(<i>&lt;MsBackendSql&gt;</i>)</a></code>
+          <code><a href="MsBackendSql.html">MsBackendSql()</a></code> <code><a href="MsBackendSql.html">createMsBackendSqlDatabase()</a></code> <code><a href="MsBackendSql.html">show(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">backendInitialize(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">dataStorage(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`[`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">extractByIndex(<i>&lt;MsBackendSql&gt;</i>,<i>&lt;ANY&gt;</i>)</a></code> <code><a href="MsBackendSql.html">peaksData(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">peaksVariables(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`intensity&lt;-`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`mz&lt;-`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`$&lt;-`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">spectraData(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">reset(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">spectraNames(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">`spectraNames&lt;-`(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterMsLevel(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterRt(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterDataOrigin(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterPrecursorMzRange(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">filterPrecursorMzValues(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">uniqueMsLevels(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">backendMerge(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">precScanNum(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">centroided(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">smoothed(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">tic(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">supportsSetBackend(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">backendBpparam(<i>&lt;MsBackendSql&gt;</i>)</a></code> <code><a href="MsBackendSql.html">dbconn(<i>&lt;MsBackendSql&gt;</i>)</a></code>
 
         </dt>
         <dd><code>Spectra</code> MS backend storing data in a SQL database</dd>
diff --git a/search.json b/search.json
index 84d60ea..f3fec8c 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Storing Mass Spectrometry Data in SQL Databases","text":"Spectra Bioconductor package provides flexible expandable infrastructure Mass Spectrometry (MS) data. package supports interchangeable use different backends provide additional file support different ways store represent MS data. MsBackendSql package provides backends store data whole MS experiments SQL databases. data databases can easily (efficiently) accessed using Spectra objects use MsBackendSql class interface data database. Spectra objects minimal memory footprint hence allow analysis large data sets even computers limited hardware capabilities. certain operations, performance data representation superior low-memory (-disk) data representations Spectra’s MsBackendMzR backend. Finally, MsBackendSql supports also remote data access e.g. central database server hosting several large MS data sets.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Storing Mass Spectrometry Data in SQL Databases","text":"package can installed BiocManager package. install BiocManager use install.packages(\"BiocManager\") , , BiocManager::install(\"MsBackendSql\") install package.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"creating-and-using-msbackendsql-sql-databases","dir":"Articles","previous_headings":"","what":"Creating and using MsBackendSql SQL databases","title":"Storing Mass Spectrometry Data in SQL Databases","text":"MsBackendSql SQL databases can created either importing (raw) MS data MS data files using createMsBackendSqlDatabase() using backendInitialize() function providing addition database connection also full MS data import DataFrame. first example use createMsBackendSqlDatabase() function takes connection (empty) database names files data imported input parameters creates necessary database tables stores full data database. create empty SQLite database (temporary file) fill MS data two mzML files (msdata package). default m/z intensity values stored BLOB data types database. advantages performance extract peaks data database example allow filter peaks m/z values directly database. alternative also possible individual m/z intensity values separate rows database table. long table format results however considerably larger databases (potentially poorer performance). Note also code backend optimized MySQL/MariaDB databases taking advantage table partitioning specialized table storage options. SQL database server however also supported (also portable, self-contained SQLite databases). MsBackendSql package provides two backends interact databases: (default) MsBackendSql class MsBackendOfflineSql, inherits properties functions former, store connection database within object connects (disconnects) () database function call. allows use latter also parallel processing setups save/load object (e.g. using save saveRDS). Thus, applications MsBackendOfflineSql might used preferred backend SQL databases. access data database create Spectra object providing connection database constructor call specifying use MsBackendSql backend using source parameter. alternative, MsBackendOfflineSql backend also used interface MS data SQL database. contrast MsBackendSql, MsBackendOfflineSql contain active (open) connection database hence supports serializing (saving) object disk using e.g. save() function, parallel processing (supported database system). Thus, use cases MsBackendOfflineSql used instead MsBackendSql. See information MsBackendOfflineSql. Spectra objects allow also change backend backend (extending MsBackend) using setBackend() function. use function first load data memory changing MsBackendSql MsBackendMemory. function also possible change backend MsBackendSql case new database created data originating backend stored database. change backend MsBackendOfflineSql need provide connection information SQL database additional parameters. parameters need passed dbConnect() call establish connection database. parameters include database driver (parameter drv), database name eventually user name, host etc (see ?dbConnect information). simple example store data SQLite database thus need provide database name, corresponds SQLite database file. example store data temporary file. Similar Spectra object can retrieve available spectra variables using spectraVariables() function. MS peak data can accessed using either mz(), intensity() peaksData() functions. extract peaks matrix 5th spectrum display first 6 rows. data (peaks data spectra variables) always retrieved fly database resulting thus minimal memory footprint Spectra object. backend supports also adding additional spectra variables changing values. add 10 seconds retention time spectrum. operations however change data database (always considered read-) cached locally within backend object (memory). size memory object thus higher changing spectra variable. $<- operations can also used cache spectra variables (temporarily) memory can eventually improve performance. test time takes extract MS level spectrum database, cache MS levels memory using $msLevel <- test timing extract cached variable. can also use reset() function reset data original state (cause local spectra variables deleted backend initialized original data database). use MsBackendOfflineSql backend need provide information required connect database along database driver Spectra function. parameters required connect database depends SQL database used driver. example data stored SQLite database, hence use SQLite() database driver need provide database name dbname parameter. MySQL/MariaDB database use MariaDB() driver provide database name, user name, password well host name port database accessible. backend provides exact functionality MsBackendSql difference connection database opened closed function call. leads slightly lower performance, allows serialize object (.e. save/load object /disk) use (hence Spectra object) also parallel processing setup. contrast, MsBackendSql parallel processing disabled since possible share active backend connection within object across different parallel processes. compare performance two backends. performance difference result opening closing database connection call. Note also depend SQL server used. SQLite databases almost overhead.","code":"library(RSQLite)  dbfile <- tempfile() con <- dbConnect(SQLite(), dbfile)  library(MsBackendSql) fls <- dir(system.file(\"sciex\", package = \"msdata\"), full.names = TRUE) createMsBackendSqlDatabase(con, fls) sps <- Spectra(con, source = MsBackendSql()) sps ## MSn data (Spectra) with 1862 spectra in a MsBackendSql backend: ##        msLevel precursorMz  polarity ##      <integer>   <numeric> <integer> ## 1            1          NA         1 ## 2            1          NA         1 ## 3            1          NA         1 ## 4            1          NA         1 ## 5            1          NA         1 ## ...        ...         ...       ... ## 1858         1          NA         1 ## 1859         1          NA         1 ## 1860         1          NA         1 ## 1861         1          NA         1 ## 1862         1          NA         1 ##  ... 34 more variables/columns. ##  Use  'spectraVariables' to list all of them. ## Database: /tmp/RtmpWP4Rr5/fileb286077e2da sps_mem <- setBackend(sps, MsBackendMemory()) sps_mem ## MSn data (Spectra) with 1862 spectra in a MsBackendMemory backend: ##        msLevel     rtime scanIndex ##      <integer> <numeric> <integer> ## 1            1     0.280         1 ## 2            1     0.559         2 ## 3            1     0.838         3 ## 4            1     1.117         4 ## 5            1     1.396         5 ## ...        ...       ...       ... ## 1858         1   258.636       927 ## 1859         1   258.915       928 ## 1860         1   259.194       929 ## 1861         1   259.473       930 ## 1862         1   259.752       931 ##  ... 34 more variables/columns. ## Processing: ##  Switch backend from MsBackendSql to MsBackendMemory [Fri Sep 27 05:10:08 2024] sps2 <- setBackend(sps_mem, MsBackendOfflineSql(), drv = SQLite(),                    dbname = tempfile()) sps2 ## MSn data (Spectra) with 1862 spectra in a MsBackendOfflineSql backend: ##        msLevel precursorMz  polarity ##      <integer>   <numeric> <integer> ## 1            1          NA         1 ## 2            1          NA         1 ## 3            1          NA         1 ## 4            1          NA         1 ## 5            1          NA         1 ## ...        ...         ...       ... ## 1858         1          NA         1 ## 1859         1          NA         1 ## 1860         1          NA         1 ## 1861         1          NA         1 ## 1862         1          NA         1 ##  ... 34 more variables/columns. ##  Use  'spectraVariables' to list all of them. ## Database: /tmp/RtmpWP4Rr5/fileb2839a46d9b ## Processing: ##  Switch backend from MsBackendSql to MsBackendMemory [Fri Sep 27 05:10:08 2024] ##  Switch backend from MsBackendMemory to MsBackendOfflineSql [Fri Sep 27 05:10:08 2024] spectraVariables(sps) ##  [1] \"msLevel\"                  \"rtime\"                    ##  [3] \"acquisitionNum\"           \"scanIndex\"                ##  [5] \"dataStorage\"              \"dataOrigin\"               ##  [7] \"centroided\"               \"smoothed\"                 ##  [9] \"polarity\"                 \"precScanNum\"              ## [11] \"precursorMz\"              \"precursorIntensity\"       ## [13] \"precursorCharge\"          \"collisionEnergy\"          ## [15] \"isolationWindowLowerMz\"   \"isolationWindowTargetMz\"  ## [17] \"isolationWindowUpperMz\"   \"peaksCount\"               ## [19] \"totIonCurrent\"            \"basePeakMZ\"               ## [21] \"basePeakIntensity\"        \"ionisationEnergy\"         ## [23] \"lowMZ\"                    \"highMZ\"                   ## [25] \"mergedScan\"               \"mergedResultScanNum\"      ## [27] \"mergedResultStartScanNum\" \"mergedResultEndScanNum\"   ## [29] \"injectionTime\"            \"filterString\"             ## [31] \"spectrumId\"               \"ionMobilityDriftTime\"     ## [33] \"scanWindowLowerLimit\"     \"scanWindowUpperLimit\"     ## [35] \"spectrum_id_\" peaksData(sps)[[5]] |> head() ##            mz intensity ## [1,] 105.0347         0 ## [2,] 105.0362       164 ## [3,] 105.0376         0 ## [4,] 105.0391         0 ## [5,] 105.0405       328 ## [6,] 105.0420         0 print(object.size(sps), units = \"KB\") ## 91.5 Kb sps$rtime <- sps$rtime + 10 print(object.size(sps), units = \"KB\") ## 106.2 Kb system.time(msLevel(sps)) ##    user  system elapsed  ##   0.007   0.001   0.008 sps$msLevel <- msLevel(sps) system.time(msLevel(sps)) ##    user  system elapsed  ##   0.002   0.000   0.002 sps <- reset(sps) sps_off <- Spectra(dbfile, drv = SQLite(),                    source = MsBackendOfflineSql()) sps_off ## MSn data (Spectra) with 1862 spectra in a MsBackendOfflineSql backend: ##        msLevel precursorMz  polarity ##      <integer>   <numeric> <integer> ## 1            1          NA         1 ## 2            1          NA         1 ## 3            1          NA         1 ## 4            1          NA         1 ## 5            1          NA         1 ## ...        ...         ...       ... ## 1858         1          NA         1 ## 1859         1          NA         1 ## 1860         1          NA         1 ## 1861         1          NA         1 ## 1862         1          NA         1 ##  ... 34 more variables/columns. ##  Use  'spectraVariables' to list all of them. ## Database: /tmp/RtmpWP4Rr5/fileb286077e2da library(microbenchmark) microbenchmark(msLevel(sps), msLevel(sps_off)) ## Unit: milliseconds ##              expr      min       lq     mean   median       uq      max neval ##      msLevel(sps) 5.332318 5.406762 5.649273 5.476532 5.542425 10.26601   100 ##  msLevel(sps_off) 6.649957 6.818596 6.973694 6.867898 6.938871 10.00390   100"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"performance-comparison-with-other-backends","dir":"Articles","previous_headings":"","what":"Performance comparison with other backends","title":"Storing Mass Spectrometry Data in SQL Databases","text":"need retrieve spectra data --fly database impact performance data access function Spectra objects using MsBackendSql backends. evaluate impact next compare performance MsBackendSql Spectra backends, specifically, MsBackendMzR default backend read represent raw MS data, MsBackendMemory backend keeps MS data memory (thus suggested larger MS experiments). Similar MsBackendMzR, also MsBackendSql keeps limited amount data memory. -disk backends need thus retrieve spectra MS peaks data --fly either original raw data files (case MsBackendMzR) SQL database (case MsBackendSql). -memory backend MsBackendMemory supposed provide fastest data access since data kept memory. thus create Spectra objects data using different backends. first compare memory footprint 3 backends. MsBackendSql lowest memory footprint 3 backends keep data memory. MsBackendMzR keeps spectra variables, except MS peaks data, memory thus larger size. MsBackendMemory keeps data (including MS peaks data) memory thus largest size memory. Next compare performance extract MS level spectrum 4 different Spectra objects. Extracting MS levels thus slowest MsBackendSql, surprising backends keep data memory MsBackendSql needs retrieve database. next compare performance access full peaks data Spectra object. expected, MsBackendMemory fasted access full peaks data. MsBackendSql outperforms however MsBackendMzR providing faster access m/z intensity values. Performance can improved MsBackendMzR using parallel processing. Note MsBackendSql support parallel processing thus parallel processing (silently) disabled functions peaksData(). next compare performance subsetting operations. two -disk backends MsBackendSql MsBackendMzR show comparable performance operation. filtering involves access spectra variables (retention time case) , MsBackendSql needs first retrieved backend. MsBackendSql backend allows however also cache spectra variables (.e. stored within MsBackendSql object). access cached spectra variables can eventually faster dedicated SQL query needed. evaluate performance pure subsetting operation first define indices 10 random spectra subset Spectra objects . MsBackendSql outperforms backends keep data memory hence need subset . two backends need subset data keep memory cases data frame either reduced set spectra variables full MS data. last compare also extraction peaks data subset Spectra objects. MsBackendSql outperforms MsBackendMzR , unexpectedly, MsBackendMemory provides fasted access.","code":"sps <- Spectra(con, source = MsBackendSql()) sps_mzr <- Spectra(fls, source = MsBackendMzR()) sps_im <- setBackend(sps_mzr, backend = MsBackendMemory()) print(object.size(sps), units = \"KB\") ## 91.5 Kb print(object.size(sps_mzr), units = \"KB\") ## 386.7 Kb print(object.size(sps_im), units = \"KB\") ## 54494.5 Kb library(microbenchmark) microbenchmark(msLevel(sps),                msLevel(sps_mzr),                msLevel(sps_im)) ## Unit: microseconds ##              expr      min        lq       mean    median        uq      max ##      msLevel(sps) 5350.232 5537.7015 5771.88027 5626.0110 5741.3965 9305.801 ##  msLevel(sps_mzr)  367.796  400.6125  432.38209  420.9550  439.0395  650.835 ##   msLevel(sps_im)   10.830   13.4655   21.04269   20.3735   23.6145   72.585 ##  neval ##    100 ##    100 ##    100 microbenchmark(peaksData(sps, BPPARAM = SerialParam()),                peaksData(sps_mzr, BPPARAM = SerialParam()),                peaksData(sps_im, BPPARAM = SerialParam()), times = 10) ## Unit: microseconds ##                                         expr        min         lq       mean ##      peaksData(sps, BPPARAM = SerialParam()) 106775.187 120725.956 285957.611 ##  peaksData(sps_mzr, BPPARAM = SerialParam()) 451588.290 456703.688 751336.931 ##   peaksData(sps_im, BPPARAM = SerialParam())    357.737    405.517   2317.596 ##      median          uq        max neval ##  350136.025  388083.791  514076.63    10 ##  770254.801 1077836.403 1114988.63    10 ##     546.204     653.339   18531.44    10 m2 <- MulticoreParam(2) microbenchmark(peaksData(sps, BPPARAM = m2),                peaksData(sps_mzr, BPPARAM = m2),                peaksData(sps_im, BPPARAM = m2), times = 10) ## Unit: microseconds ##                              expr        min         lq        mean      median ##      peaksData(sps, BPPARAM = m2)  96809.705 106153.578 171793.8454 125550.1305 ##  peaksData(sps_mzr, BPPARAM = m2) 463529.496 485036.802 675009.7979 649723.4730 ##   peaksData(sps_im, BPPARAM = m2)    383.796    618.193    605.1018    644.4725 ##          uq         max neval ##  133632.325  396552.127    10 ##  783405.630 1125822.560    10 ##     674.268     724.341    10 microbenchmark(filterRt(sps, rt = c(50, 100)),                filterRt(sps_mzr, rt = c(50, 100)),                filterRt(sps_im, rt = c(50, 100))) ## Unit: microseconds ##                                expr      min       lq      mean   median ##      filterRt(sps, rt = c(50, 100)) 2685.972 2748.231 2976.2252 2797.785 ##  filterRt(sps_mzr, rt = c(50, 100)) 2030.728 2141.570 2333.1756 2206.873 ##   filterRt(sps_im, rt = c(50, 100))  452.784  485.421  522.1169  507.597 ##         uq       max neval ##  2861.4985 17459.073   100 ##  2421.4225  6680.685   100 ##   548.1525   895.580   100 idx <- sample(seq_along(sps), 10) microbenchmark(sps[idx],                sps_mzr[idx],                sps_im[idx]) ## Unit: microseconds ##          expr     min       lq     mean   median       uq     max neval ##      sps[idx] 132.798 141.6640 152.3949 150.5610 157.0680 280.623   100 ##  sps_mzr[idx] 643.571 669.1335 685.4696 678.8715 694.1505 927.961   100 ##   sps_im[idx] 223.306 234.2920 243.9662 241.7510 250.4520 367.947   100 sps_10 <- sps[idx] sps_mzr_10 <- sps_mzr[idx] sps_im_10 <- sps_im[idx]  microbenchmark(peaksData(sps_10),                peaksData(sps_mzr_10),                peaksData(sps_im_10),                times = 10) ## Unit: microseconds ##                   expr      min        lq       mean    median        uq ##      peaksData(sps_10)  2647.50  2654.273  3291.1344  3614.394  3715.712 ##  peaksData(sps_mzr_10) 69819.87 72925.655 73515.5042 73877.762 74639.904 ##   peaksData(sps_im_10)   348.27   406.358   510.9153   447.791   612.092 ##        max neval ##   3878.386    10 ##  75518.083    10 ##    863.561    10"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"considerations-for-database-systemsservers","dir":"Articles","previous_headings":"Performance comparison with other backends","what":"Considerations for database systems/servers","title":"Storing Mass Spectrometry Data in SQL Databases","text":"backends MsBackendSql package use standard SQL calls retrieve MS data database hence SQL database system (R package available) supported. SQLite-based databases represent easiest user friendly solution since database server administration user management required. Indeed, performance SQLite high, even large data sets. Server-based databases hand advantage enable centralized storage control MS data (inclusive user management etc). Also, server systems also allow data set server-specific configurations improve performance. comparison SQLite-based MariaDB-based MsBackendSql database large data set comprising 8,000 samples 15,000,000 spectra available . brief, performance extract data comparable individual spectra variables even faster SQLite database. complex SQL queries involved (combining several primary keys data fields) advanced MariaDB database outperformed SQLite.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"other-properties-of-the-msbackendsql","dir":"Articles","previous_headings":"","what":"Other properties of the MsBackendSql","title":"Storing Mass Spectrometry Data in SQL Databases","text":"MsBackendSql backend support parallel processing since database connection can shared across different (parallel) processes. Thus, methods Spectra objects use MsBackendSql automatically (silently) disable parallel processing even dedicated parallel processing setup passed along BPPARAM method. functions Spectra objects require load MS peak data (.e., m/z intensity values) memory. large data sets (computers limited hardware resources) function calls can cause --memory errors. One example lengths() function determines number peaks per spectrum loading peak matrix first memory. functions ideally called using peaksapply() function parameter chunkSize (e.g., peaksapply(sps, lengths, chunkSize = 5000L)). Instead processing full data set, data first split chunks size chunkSize stepwise processed. Hence, data chunkSize spectra loaded memory one iteration.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Storing Mass Spectrometry Data in SQL Databases","text":"MsBackendSql provides MS data representations storage mode minimal memory footprint (R) still comparably efficient standard processing subsetting operations. backend specifically useful large MS data sets, even hosted remote (MySQL/MariaDB) servers. potential use case backend thus set central storage place MS experiments data analysts connecting remotely server perform initial data exploration filtering. subsetting smaller data set interest, users retrieve/download data changing backend e.g. MsBackendMemory, result download full data user computer’s memory.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"session-information","dir":"Articles","previous_headings":"","what":"Session information","title":"Storing Mass Spectrometry Data in SQL Databases","text":"","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C             ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats4    stats     graphics  grDevices utils     datasets  methods   ## [8] base      ##  ## other attached packages: ## [1] microbenchmark_1.5.0 RSQLite_2.3.7        MsBackendSql_1.5.0   ## [4] Spectra_1.15.8       ProtGenerics_1.37.1  BiocParallel_1.39.0  ## [7] S4Vectors_0.43.2     BiocGenerics_0.51.1  BiocStyle_2.33.1     ##  ## loaded via a namespace (and not attached): ##  [1] sass_0.4.9             MsCoreUtils_1.17.2     hms_1.1.3              ##  [4] digest_0.6.37          evaluate_1.0.0         bookdown_0.40          ##  [7] fastmap_1.2.0          blob_1.2.4             jsonlite_1.8.9         ## [10] progress_1.2.3         mzR_2.39.0             DBI_1.2.3              ## [13] BiocManager_1.30.25    codetools_0.2-20       textshaping_0.4.0      ## [16] jquerylib_0.1.4        cli_3.6.3              rlang_1.1.4            ## [19] crayon_1.5.3           Biobase_2.65.1         bit64_4.5.2            ## [22] cachem_1.1.0           yaml_2.3.10            tools_4.4.1            ## [25] parallel_4.4.1         memoise_2.0.1          ncdf4_1.23             ## [28] vctrs_0.6.5            R6_2.5.1               lifecycle_1.0.4        ## [31] fs_1.6.4               htmlwidgets_1.6.4      IRanges_2.39.2         ## [34] bit_4.5.0              clue_0.3-65            MASS_7.3-61            ## [37] ragg_1.3.3             cluster_2.1.6          pkgconfig_2.0.3        ## [40] desc_1.4.3             pkgdown_2.1.1.9000     bslib_0.8.0            ## [43] Rcpp_1.0.13            data.table_1.16.0      systemfonts_1.1.0      ## [46] xfun_0.47              knitr_1.48             htmltools_0.5.8.1      ## [49] rmarkdown_2.28         compiler_4.4.1         prettyunits_1.2.0      ## [52] MetaboCoreUtils_1.13.0"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Rainer. Author, maintainer. Chong Tang. Contributor. Laurent Gatto. Contributor.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Rainer J (2024). MsBackendSql: SQL-based Mass Spectrometry Data Backend. R package version 1.5.0, https://github.com/RforMassSpectrometry/MsBackendSql.","code":"@Manual{,   title = {MsBackendSql: SQL-based Mass Spectrometry Data Backend},   author = {Johannes Rainer},   year = {2024},   note = {R package version 1.5.0},   url = {https://github.com/RforMassSpectrometry/MsBackendSql}, }"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"sql-based-mass-spectrometry-data-backend","dir":"","previous_headings":"","what":"SQL-based Mass Spectrometry Data Backend","title":"SQL-based Mass Spectrometry Data Backend","text":"repository provides backend Spectra objects supports storage mass spectrometry (MS) data SQL database. package provides functionality create databases original (raw) MS data files (mzML, mzXML netCDF format) allows extract data efficient way. information see package homepage.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"creating-a-database","dir":"","previous_headings":"","what":"Creating a database","title":"SQL-based Mass Spectrometry Data Backend","text":"providing connection SQL database, createMsBackendSqlDatabase imports raw MS data provided file names stores dedicated database tables created import. MsBackendSql supports type SQL database, currently optimized MySQL/MariaDB databases.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"using-a-msbackendsql-database","dir":"","previous_headings":"","what":"Using a MsBackendSql database","title":"SQL-based Mass Spectrometry Data Backend","text":"MS data MsBackendSql database can accessed Spectra package using MsBackendSql MS backend. Assuming variable dbcon represents (RDBI) database connection MsBackendSql, data can represented/used Spectra object : information see package homepage.","code":"library(Spectra) library(MsBackendSql) sps <- Spectra(dbcon, source = MsBackendSql())"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"SQL-based Mass Spectrometry Data Backend","text":"package can installed ","code":"install.packages(\"BiocManager\") BiocManager::install(\"MsBackendSql\")"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"contributions","dir":"","previous_headings":"","what":"Contributions","title":"SQL-based Mass Spectrometry Data Backend","text":"Contributions highly welcome follow contribution guidelines. Also, please check coding style guidelines RforMassSpectrometry vignette.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":null,"dir":"Reference","previous_headings":"","what":"SQL-based MS backend without active database connection — MsBackendOfflineSql","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"MsBackendOfflineSql backend extends MsBackendSql() backend directly inherits thus functions well properties. difference two backend MsBackendSql keeps active connection SQL database inside object MsBackendOfflineSql backends reconnects SQL database query. performance latter slightly lower (due need connect/disconnect database function call) can also used parallel processing environment.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"","code":"MsBackendOfflineSql()  # S4 method for class 'MsBackendOfflineSql' backendInitialize(   object,   drv = NULL,   dbname = character(),   user = character(),   password = character(),   host = character(),   port = NA_integer_,   data,   ... )"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"object MsBackendOfflineSql object. drv DBI database driver object (SQLite() RSQLite package MariaDB() RMariaDB package). See dbConnect() information. dbname character(1) name database. Passed directly dbConnect(). user character(1) user name database. Passed directly dbConnect(). password character(1) password database. Note password stored (unencrypted) within object. Passed directly dbConnect(). host character(1) host running database. Passed directly dbConnect(). port integer(1) port number (optional). Passed directly dbConnect(). data backendInitialize(): optional DataFrame full spectra data inserted (new) MsBackendSql database. provided, assumed provided database connection information (writeable) empty database data inserted. data output spectraData another backend. ... ignored.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":"creation-of-backend-objects","dir":"Reference","previous_headings":"","what":"Creation of backend objects","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"empty instance MsBackendOfflineSql class can created using MsBackendOfflineSql() function. existing MsBackendSql SQL database can loaded backendInitialize() function. function takes parameters drv, dbname, user, password, host port, parameters passed dbConnect() function connect (existing) SQL database. See MsBackendSql() information create MsBackend SQL database.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"Johannes Rainer","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":null,"dir":"Reference","previous_headings":"","what":"Spectra MS backend storing data in a SQL database — MsBackendSql","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"MsBackendSql implementation MsBackend() class Spectra() objects stores retrieves MS data SQL database. New databases can created raw MS data files using createMsBackendSqlDatabase().","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"","code":"MsBackendSql()  createMsBackendSqlDatabase(   dbcon,   x = character(),   backend = MsBackendMzR(),   chunksize = 10L,   blob = TRUE,   partitionBy = c(\"none\", \"spectrum\", \"chunk\"),   partitionNumber = 10L )  # S4 method for class 'MsBackendSql' show(object)  # S4 method for class 'MsBackendSql' backendInitialize(object, dbcon, data, ...)  # S4 method for class 'MsBackendSql' dataStorage(object)  # S4 method for class 'MsBackendSql' x[i, j, ..., drop = FALSE]  # S4 method for class 'MsBackendSql' peaksData(object, columns = c(\"mz\", \"intensity\"))  # S4 method for class 'MsBackendSql' peaksVariables(object)  # S4 method for class 'MsBackendSql' intensity(object) <- value  # S4 method for class 'MsBackendSql' mz(object) <- value  # S4 method for class 'MsBackendSql' x$name <- value  # S4 method for class 'MsBackendSql' spectraData(object, columns = spectraVariables(object))  # S4 method for class 'MsBackendSql' reset(object)  # S4 method for class 'MsBackendSql' spectraNames(object)  # S4 method for class 'MsBackendSql' spectraNames(object) <- value  # S4 method for class 'MsBackendSql' filterMsLevel(object, msLevel = uniqueMsLevels(object))  # S4 method for class 'MsBackendSql' filterRt(object, rt = numeric(), msLevel. = integer())  # S4 method for class 'MsBackendSql' filterDataOrigin(object, dataOrigin = character())  # S4 method for class 'MsBackendSql' filterPrecursorMzRange(object, mz = numeric())  # S4 method for class 'MsBackendSql' filterPrecursorMzValues(object, mz = numeric(), ppm = 20, tolerance = 0)  # S4 method for class 'MsBackendSql' uniqueMsLevels(object, ...)  # S4 method for class 'MsBackendSql' backendMerge(object, ...)  # S4 method for class 'MsBackendSql' precScanNum(object)  # S4 method for class 'MsBackendSql' centroided(object)  # S4 method for class 'MsBackendSql' smoothed(object)  # S4 method for class 'MsBackendSql' tic(object, initial = TRUE)  # S4 method for class 'MsBackendSql' supportsSetBackend(object, ...)  # S4 method for class 'MsBackendSql' backendBpparam(object, BPPARAM = bpparam())  # S4 method for class 'MsBackendSql' dbconn(x)"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"dbcon Connection database. x createMsBackendSqlDatabase(): character names raw data files data imported. methods MsqlBackend instance. backend createMsBackendSqlDatabase(): MS backend can used import MS data raw files specified parameter x. chunksize createMsBackendSqlDatabase(): integer(1) defining number input processed per iteration. chunksize = 1 file specified x imported data inserted database. chunksize = 5 data 5 files imported (parallel) inserted database. Thus, higher values might result faster database creation, require also memory. blob createMsBackendSqlDatabase(): logical(1) whether individual m/z intensity values stored separately (blob = FALSE) m/z intensity values spectrum stored single BLOB SQL data type (blob = TRUE, default). partitionBy createMsBackendSqlDatabase(): character(1) defining peak data table partitioned. \"none\" (default): partitioning, \"spectrum\": peaks assigned partition based spectrum ID (number), .e. spectra evenly (consecutively) assigned across partitions. partitionNumber = 3, first spectrum assigned first partition, second second, third third fourth spectrum first partition. \"chunk\": spectra processed part chunk placed partition. spectra next processed chunk assigned next partition. Note available MySQL/MariaDB databases, .e., con MariaDBConnection. See details information. partitionNumber createMsBackendSqlDatabase(): integer(1) defining number partitions database table partitioned (supported MySQL/MariaDB databases). object MsBackendSql instance. data backendInitialize(): optional DataFrame full spectra data inserted (new) MsBackendSql database. provided, assumed dbcon (writeable) connection empty database data inserted. data output spectraData another backend. ... [: ignored. backendInitialize, parameter data used: additional parameters passed function creating database blob. [: integer logical subset object. j [: ignored. drop [: logical(1), ignored. columns spectraData(): character() optionally defining subset spectra variables returned. Defaults columns = spectraVariables(object) hence variables returned. peaksData accessor: optional character requested columns individual matrix returned list. Defaults columns = c(\"mz\", \"intensity\") columns listed peaksVariables supported. value setter methods: replacement value. name <-: character(1) name spectra variable replace. msLevel filterMsLevel(): integer specifying MS levels filter data. rt filterRt(): numeric(2) lower upper retention time. Spectra retention time >= rt[1] <= rt[2] returned. msLevel. filterRt(): integerwith MS level(s) retention time filter applied (spectra MS levels considered filter returned **). specified, retention time filter applied MS levels inobject`. dataOrigin filterDataOrigin(): character data origin values data subsetted. mz filterPrecursorMzRange(): numeric(2) desired lower upper limit precursor m/z range. filterPrecursorMzValues(): numeric m/z value(s) filter object. ppm filterPrecursorMzValues(): numeric m/z-relative maximal acceptable difference m/z value considered matching. Can length 1 equal length(mz). tolerance filterPrecursorMzValues(): numeric absolute difference m/z values considered matching. Can length 1 equal length(mz). initial tic(): logical(1) whether original total ion count returned (initial = TRUE, default) whether calculated spectras' intensities (initial = FALSE). BPPARAM backendBpparam(): BiocParallel parallel processing setup. See bpparam() information.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"See documentation respective function.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"MsBackendSql class principally read-backend extending MsBackendCached() backend Spectra package allows changing adding (temporarily) spectra variables without changing original data SQL database.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"MsBackendSql backend keeps (open) connection SQL database data hence support saving/loading backend disk (e.g. using save saveRDS). Also, reason, MsBackendSql support parallel processing. backendBpparam() method MsBackendSql thus always return SerialParam() object. MsBackendOfflineSql() used alternative supports saving/loading data /disk supports also parallel processing.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"creation-of-backend-objects","dir":"Reference","previous_headings":"","what":"Creation of backend objects","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"New backend objects can created MsBackendSql() function. SQL databases can created filled MS data raw data files using createMsBackendSqlDatabase() function using backendInitialize() providing data parameter data. addition possible create database Spectra object changing backend MsBackendSql MsBackendOfflineSql using setBackend() function. Existing SQL databases (created previously createMsBackendSqlDatabase() backendInitialize() data parameter) can loaded using conventional way create/initialize MsBackend classes, .e. using backendInitialize(). createMsBackendSqlDatabase(): create database fill MS data. Parameter dbcon expected database connection, parameter x character vector file names import data. Parameter backend used actual data import defaults backend = MsBackendMzR() hence allowing import data mzML, mzXML netCDF files. Parameter chunksize allows define number files (x) data imported one iteration. default chunksize = 10L data imported 10 files x time (backend supports even parallel) data inserted database. Larger chunk sizes require memory also larger disk space (data import performed temporary files) might eventually faster. Parameter blob allows define whether m/z intensity values spectrum stored BLOB SQL data type database (blob = TRUE, default) individual m/z intensity values peak stored separately (blob = FALSE). latter case results much larger database slower performance peaksData function, allow define custom (manual) SQL queries individual peak values. data can stored SQL database, present suggested use MySQL/MariaDB databases. dbcon connection MySQL/MariaDB database, tables use ARIA engine providing faster data access use table partitioning: tables splitted multiple partitions can improve data insertion index generation. Partitioning can defined parameters partitionBy partitionNumber. default partitionBy = \"none\" partitioning performed. blob = TRUE partitioning usually required. blob = FALSE  large datasets suggested enable table partitioning selecting either partitionBy = \"spectrum\" partitionBy = \"chunk\". first option assignes consecutive spectra different partitions latter puts spectra files part chunk partition. options performance partitionBy = \"spectrum\" requires less disk space. Note , inserting data takes considerable amount time, also subsequent creation database indices can take long (even longer data insertion blob = FALSE). backendInitialize(): get access initialize MsBackendSql object. Parameter object supposed MsBackendSql instance, created e.g. MsBackendSql(). Parameter dbcon expected connection existing MsBackendSql SQL database (created e.g. createMsBackendSqlDatabase()). backendInitialize() can alternatively also used create new MsBackendSql database using optional data parameter. case, dbcon expected writeable connection empty database data DataFrame full spectra data inserted database. format data match format DataFrame returned spectraData() function requires columns \"mz\" \"intensity\" m/z intensity values spectrum. backendInitialize() call create necessary tables database, fill tables provided data return MsBackendSql database. Thus, MsBackendSql supports setBackend method Spectra change () backend MsBackendSql. Note however chunk-wise (parallel) processing needs disabled case passing eventually f = factor() setBackend() call. supportsSetBackend(): whether MsBackendSql supports setBackend() method change MsBackend Spectra object MsBackendSql. Returns TRUE, thus, changing backend MsBackendSql supported writeable database connection provided addition parameter dbcon (.e. setBackend(sps, MsBackendSql(), dbcon = con) con connection empty database store full spectra data Spectra object sps specified database return Spectra object uses MsBackendSql). backendBpparam(): whether MsBackendSql supports parallel processing. Takes MsBackendSql parallel processing setup (see bpparam() details) input always returns SerialParam() since MsBackendSql support parallel processing. dbconn(): returns connection database.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"subsetting-merging-and-filtering-data","dir":"Reference","previous_headings":"","what":"Subsetting, merging and filtering data","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"MsBackendSql objects can subsetted using [ function. Internally, simply subset integer vector primary keys eventually cached data. original data database affected subsetting operation. subsetting operation can undone resetting object reset() function. Subsetting arbitrary order well index replication supported. Multiple MsBackendSql objects can also merged (combined) backendMerge() function. Note requires MsBackendSql objects connected database. function thus mostly used combining MsBackendSql objects previously splitted using e.g. split(). addition, MsBackendSql supports filtering methods available MsBackendCached(). Implementation filter functions optimized MsBackendSql objects : filterDataOrigin(): filter object retaining spectra dataOrigin spectra variable values matching provided ones parameter dataOrigin. function returns results order values provided parameter dataOrigin. filterMsLevel(): filter object based MS levels specified parameter msLevel. function filtering using SQL queries. \"msLevel\" local variable stored within object (hence memory) default implementation MsBackendCached used instead. filterPrecursorMzRange(): filters data keeping spectra precursorMz within m/z value range provided parameter mz (.e. spectra precursor m/z >= mz[1L] <= mz[2L]). filterPrecursorMzValues(): filters data keeping spectra precursor m/z values matching value(s) provided parameter mz. Parameters ppmandtoleranceallow specify acceptable differences compared values. Lengths ofppmandtolerancecan either1or equal tolength(mz)` use different values ppm tolerance provided m/z value. filterRt(): filter object keeping spectra retention times within specified retention time range (parameter rt). Optional parameter msLevel. allows restrict retention time filter provided MS level(s) returning spectra MS levels.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"accessing-and-modifying-data","dir":"Reference","previous_headings":"","what":"Accessing and modifying data","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"functions listed specifically implemented MsBackendSql. addition, MsBackendSql inherits supports data accessor, filtering functions data manipulation functions MsBackendCached(). $, $<-: access set (add) spectra variables object. Spectra variables added modified using $<- cached locally within object (data database never changed). restore object (.e. drop cached values) reset function can used. dataStorage(): returns character vector length spectra object name database containing data. intensity<-: supported. mz<-: supported. peaksData(): returns list spectras' peak data. length list equal number spectra object. element list matrix columns according parameter columns. empty spectrum, matrix 0 rows returned. Use peaksVariables(object) list supported values parameter columns. peaksVariables(): returns character available peak variables, .e. columns queried peaksData(). reset(): restores MsBackendSql re-initializing data database. subsetting cached spectra variables lost. spectraData(): gets general spectrum metadata. spectraData() returns DataFrame number rows spectra object. Parameter columns allows select specific spectra variables. spectraNames(), spectraNames<-: returns character length equal number spectra object primary keys spectra database (converted character). Replacing spectra names spectraNames<- supported. uniqueMsLevels(): returns unique MS levels spectra object. tic(): returns originally reported total ion count (initial = TRUE) calculates total ion count intensities spectrum (initial = FALSE).","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"implementation-notes","dir":"Reference","previous_headings":"","what":"Implementation notes","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"Internally, MsBackendSql class contains primary keys spectra stored SQL database. Keeping integer memory guarantees minimal memory footpring object. Still, depending number spectra database, integer vector might become large. data access involve SQL calls retrieve data database. extending MsBackendCached() object Spectra package, MsBackendSql supports (temporarily, .e. duration R session) add modify spectra variables. however stored data.frame within object thus increasing memory demand object.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"Johannes Rainer","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"","code":"#### ## Create a new MsBackendSql database  ## Define a file from which to import the data data_file <- system.file(\"microtofq\", \"MM8.mzML\", package = \"msdata\")  ## Create a database/connection to a database library(RSQLite) db_file <- tempfile() dbc <- dbConnect(SQLite(), db_file)  ## Import the data from the file into the database createMsBackendSqlDatabase(dbc, data_file) #> Importing data ...  #>  #> [==========================================================] 1/1 (100%) in  1s #>  #> Creating indices  #> . #> . #> . #> . #>  Done #> [1] TRUE dbDisconnect(dbc)  ## Initialize a MsBackendSql dbc <- dbConnect(SQLite(), db_file) be <- backendInitialize(MsBackendSql(), dbc)  be #> MsBackendSql with 198 spectra #>       msLevel precursorMz  polarity #>     <integer>   <numeric> <integer> #> 1           1          NA         1 #> 2           1          NA         1 #> 3           1          NA         1 #> 4           1          NA         1 #> 5           1          NA         1 #> ...       ...         ...       ... #> 194         1          NA         1 #> 195         1          NA         1 #> 196         1          NA         1 #> 197         1          NA         1 #> 198         1          NA         1 #>  ... 34 more variables/columns. #>  Use  'spectraVariables' to list all of them. #> Database: /tmp/RtmpqLniVu/filea684cdb5a7b  ## Original data source head(be$dataOrigin) #> [1] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [2] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [3] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [4] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [5] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [6] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\"  ## Data storage head(dataStorage(be)) #> [1] \"/tmp/RtmpqLniVu/filea684cdb5a7b\" \"/tmp/RtmpqLniVu/filea684cdb5a7b\" #> [3] \"/tmp/RtmpqLniVu/filea684cdb5a7b\" \"/tmp/RtmpqLniVu/filea684cdb5a7b\" #> [5] \"/tmp/RtmpqLniVu/filea684cdb5a7b\" \"/tmp/RtmpqLniVu/filea684cdb5a7b\"  ## Access all spectra data spd <- spectraData(be) spd #> DataFrame with 198 rows and 37 columns #>       msLevel     rtime acquisitionNum scanIndex                             mz #>     <integer> <numeric>      <integer> <integer>                  <NumericList> #> 1           1     0.486              1         1    104.554,106.996,107.966,... #> 2           1     0.822              2         2    107.960,109.964,112.027,... #> 3           1     1.159              3         3    107.963,112.021,113.035,... #> 4           1     1.495              4         4    105.971,109.984,112.028,... #> 5           1     1.832              5         5    104.474,107.000,109.968,... #> ...       ...       ...            ...       ...                            ... #> 194         1   65.4360            194       194    106.992,111.459,112.022,... #> 195         1   65.7720            195       195  99.0797,109.0031,112.0232,... #> 196         1   66.1092            196       196    102.927,108.970,112.028,... #> 197         1   66.4458            197       197    111.058,112.026,113.029,... #> 198         1   66.7818            198       198    111.044,112.024,112.518,... #>           intensity            dataStorage             dataOrigin centroided #>       <NumericList>            <character>            <character>  <logical> #> 1      23,35,50,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #> 2    35, 24,140,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #> 3    28,179,350,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #> 4    25, 28,131,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #> 5      26,30,25,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #> ...             ...                    ...                    ...        ... #> 194    34,24,86,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #> 195  24, 22,198,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #> 196    29,22,98,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #> 197  31,124,189,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #> 198    67,84,22,... /tmp/RtmpqLniVu/file.. /__w/_temp/Library/m..       TRUE #>      smoothed  polarity precScanNum precursorMz precursorIntensity #>     <logical> <integer>   <integer>   <numeric>          <numeric> #> 1          NA         1          NA          NA                 NA #> 2          NA         1          NA          NA                 NA #> 3          NA         1          NA          NA                 NA #> 4          NA         1          NA          NA                 NA #> 5          NA         1          NA          NA                 NA #> ...       ...       ...         ...         ...                ... #> 194        NA         1          NA          NA                 NA #> 195        NA         1          NA          NA                 NA #> 196        NA         1          NA          NA                 NA #> 197        NA         1          NA          NA                 NA #> 198        NA         1          NA          NA                 NA #>     precursorCharge collisionEnergy isolationWindowLowerMz #>           <integer>       <numeric>              <numeric> #> 1                NA              NA                     NA #> 2                NA              NA                     NA #> 3                NA              NA                     NA #> 4                NA              NA                     NA #> 5                NA              NA                     NA #> ...             ...             ...                    ... #> 194              NA              NA                     NA #> 195              NA              NA                     NA #> 196              NA              NA                     NA #> 197              NA              NA                     NA #> 198              NA              NA                     NA #>     isolationWindowTargetMz isolationWindowUpperMz peaksCount totIonCurrent #>                   <numeric>              <numeric>  <integer>     <numeric> #> 1                        NA                     NA       1743         97322 #> 2                        NA                     NA       1708         98590 #> 3                        NA                     NA       1708         96425 #> 4                        NA                     NA       1747         97144 #> 5                        NA                     NA       1730         94631 #> ...                     ...                    ...        ...           ... #> 194                      NA                     NA       2267        142472 #> 195                      NA                     NA       2488        167102 #> 196                      NA                     NA       2324        137565 #> 197                      NA                     NA       2105        113086 #> 198                      NA                     NA       1996         97257 #>     basePeakMZ basePeakIntensity ionisationEnergy     lowMZ    highMZ #>      <numeric>         <numeric>        <numeric> <numeric> <numeric> #> 1      144.050              7250                0   104.554  1004.470 #> 2      144.050              7064                0   107.960  1002.799 #> 3      144.050              7124                0   107.963   993.959 #> 4      144.051              7067                0   105.971   986.756 #> 5      144.051              6891                0   104.474  1003.469 #> ...        ...               ...              ...       ...       ... #> 194    144.051              4615                0  106.9921  1003.828 #> 195    144.051              3812                0   99.0797  1003.270 #> 196    144.050              3526                0  102.9272  1000.594 #> 197    144.050              3902                0  111.0582   984.228 #> 198    144.051              3587                0  111.0437  1000.851 #>     mergedScan mergedResultScanNum mergedResultStartScanNum #>      <integer>           <integer>                <integer> #> 1           NA                  NA                       NA #> 2           NA                  NA                       NA #> 3           NA                  NA                       NA #> 4           NA                  NA                       NA #> 5           NA                  NA                       NA #> ...        ...                 ...                      ... #> 194         NA                  NA                       NA #> 195         NA                  NA                       NA #> 196         NA                  NA                       NA #> 197         NA                  NA                       NA #> 198         NA                  NA                       NA #>     mergedResultEndScanNum injectionTime filterString  spectrumId #>                  <integer>     <numeric>  <character> <character> #> 1                       NA             0           NA      scan=1 #> 2                       NA             0           NA      scan=2 #> 3                       NA             0           NA      scan=3 #> 4                       NA             0           NA      scan=4 #> 5                       NA             0           NA      scan=5 #> ...                    ...           ...          ...         ... #> 194                     NA             0           NA    scan=194 #> 195                     NA             0           NA    scan=195 #> 196                     NA             0           NA    scan=196 #> 197                     NA             0           NA    scan=197 #> 198                     NA             0           NA    scan=198 #>     ionMobilityDriftTime scanWindowLowerLimit scanWindowUpperLimit spectrum_id_ #>                <numeric>            <numeric>            <numeric>    <integer> #> 1                     NA                   NA                   NA            1 #> 2                     NA                   NA                   NA            2 #> 3                     NA                   NA                   NA            3 #> 4                     NA                   NA                   NA            4 #> 5                     NA                   NA                   NA            5 #> ...                  ...                  ...                  ...          ... #> 194                   NA                   NA                   NA          194 #> 195                   NA                   NA                   NA          195 #> 196                   NA                   NA                   NA          196 #> 197                   NA                   NA                   NA          197 #> 198                   NA                   NA                   NA          198  ## Available variables spectraVariables(be) #>  [1] \"msLevel\"                  \"rtime\"                    #>  [3] \"acquisitionNum\"           \"scanIndex\"                #>  [5] \"mz\"                       \"intensity\"                #>  [7] \"dataStorage\"              \"dataOrigin\"               #>  [9] \"centroided\"               \"smoothed\"                 #> [11] \"polarity\"                 \"precScanNum\"              #> [13] \"precursorMz\"              \"precursorIntensity\"       #> [15] \"precursorCharge\"          \"collisionEnergy\"          #> [17] \"isolationWindowLowerMz\"   \"isolationWindowTargetMz\"  #> [19] \"isolationWindowUpperMz\"   \"peaksCount\"               #> [21] \"totIonCurrent\"            \"basePeakMZ\"               #> [23] \"basePeakIntensity\"        \"ionisationEnergy\"         #> [25] \"lowMZ\"                    \"highMZ\"                   #> [27] \"mergedScan\"               \"mergedResultScanNum\"      #> [29] \"mergedResultStartScanNum\" \"mergedResultEndScanNum\"   #> [31] \"injectionTime\"            \"filterString\"             #> [33] \"spectrumId\"               \"ionMobilityDriftTime\"     #> [35] \"scanWindowLowerLimit\"     \"scanWindowUpperLimit\"     #> [37] \"spectrum_id_\"              ## Access mz values mz(be) #> NumericList of length 198 #> [[1]] 104.553733825684 106.996170043945 ... 1002.67761230469 1004.47033691406 #> [[2]] 107.959617614746 109.964324951172 ... 991.343811035156 1002.79937744141 #> [[3]] 107.962753295898 112.021392822266 ... 964.238586425781 993.959167480469 #> [[4]] 105.970863342285 109.984230041504 ... 979.084838867188 986.755981445312 #> [[5]] 104.473876953125 106.999610900879 ... 1003.185546875 1003.46936035156 #> [[6]] 102.036674499512 107.963928222656 ... 993.781127929688 994.755920410156 #> [[7]] 104.272621154785 112.024925231934 ... 996.248046875 1001.64440917969 #> [[8]] 98.9297180175781 106.506416320801 ... 991.034484863281 997.045837402344 #> [[9]] 107.966445922852 109.385284423828 ... 995.031494140625 995.600463867188 #> [[10]] 108.965042114258 109.974197387695 ... 982.596313476562 989.777404785156 #> ... #> <188 more elements>  ## Subset the object to spectra in arbitrary order be_sub <- be[c(5, 1, 1, 2, 4, 100)] be_sub #> MsBackendSql with 6 spectra #>     msLevel precursorMz  polarity #>   <integer>   <numeric> <integer> #> 1         1          NA         1 #> 2         1          NA         1 #> 3         1          NA         1 #> 4         1          NA         1 #> 5         1          NA         1 #> 6         1          NA         1 #>  ... 34 more variables/columns. #>  Use  'spectraVariables' to list all of them. #> Database: /tmp/RtmpqLniVu/filea684cdb5a7b  ## The internal spectrum IDs (primary keys from the database) be_sub$spectrum_id_ #> [1]   5   1   1   2   4 100  ## Add additional spectra variables be_sub$new_variable <- \"B\"  ## This variable is *cached* locally within the object (not inserted into ## the database) be_sub$new_variable #> [1] \"B\" \"B\" \"B\" \"B\" \"B\" \"B\""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.5","title":"MsBackendSql 1.3","text":"Improve input argument check error message backendInitialize() MsBackendOfflineSql. Update documentation adding () function names.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3-1","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.4","title":"MsBackendSql 1.3","text":"Ensure primary keys database correct order backendInitialize().","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3-2","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.3","title":"MsBackendSql 1.3","text":"Import method generics ProtGenerics.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3-3","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.2","title":"MsBackendSql 1.3","text":"Add dedicated setBackend method MsBackendSql MsBackendOfflineSql backends (issue #17).","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3-4","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.1","title":"MsBackendSql 1.3","text":"Add description use/advantages different SQL database systems vignette.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.5","title":"MsBackendSql 1.1","text":"Add dbconn methods MsBackendSql MsBackendOfflineSql.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1-1","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.4","title":"MsBackendSql 1.1","text":"Improve performance createMsBackendSqlDatabase using also parallel processing peaksData call.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1-2","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.3","title":"MsBackendSql 1.1","text":"Add support setBackend MsBackendOfflineSql.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1-3","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.2","title":"MsBackendSql 1.1","text":"Mention documentation MsBackendSql can saved disk. Expand vignette adding related documentation.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1-4","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.1","title":"MsBackendSql 1.1","text":"Fix filterRt avoiding filter range infinite.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.7","title":"MsBackendSql 0.99","text":"Decrease required R version 4.2.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-1","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.6","title":"MsBackendSql 0.99","text":"Add mzR Suggests ensure package vignettes can build properly.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-2","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.5","title":"MsBackendSql 0.99","text":"Add MsBackendOfflineSql backend re-connects database query.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-3","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.4","title":"MsBackendSql 0.99","text":"Add backendBpparam method ensure parallel processing disabled MsBackendSql backend.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-4","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.3","title":"MsBackendSql 0.99","text":"Add backendMerge method. Add parameter data backendInitialize allow creating new MsBackendSql database store values data . enables use Spectra,setBackend convert backend MsBackendSql. Implement supportsSetBackend enable setBackend,Spectra,MsBackendSql.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-5","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.2","title":"MsBackendSql 0.99","text":"Evaluate validity MsBackendSql using full unit test suite Spectra package.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-6","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.1","title":"MsBackendSql 0.99","text":"Address Kayla’s package review comments.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-7","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.0","title":"MsBackendSql 0.99","text":"Prepare package submission Bioconductor.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-98","dir":"Changelog","previous_headings":"","what":"Changes in 0.98.1","title":"MsBackendSql 0.98","text":"Rename MsqlBackend MsBackendSql.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-98-1","dir":"Changelog","previous_headings":"","what":"Changes in 0.98.0","title":"MsBackendSql 0.98","text":"Add vignette.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-1","dir":"Changelog","previous_headings":"","what":"Changes in 0.1.0","title":"MsBackendSql 0.1","text":"Add parameter blob allow storing m/z intensity values BLOB data type database. MsBackendSql use different functions retrieve data database type storage.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-0","dir":"Changelog","previous_headings":"","what":"Changes in 0.0.5","title":"MsBackendSql 0.0","text":"Add filterMsLevel method. Add filterRt method. Add filterDataOrigin method. Add filterPrecursorMzRange method. Add filterPrecursorMzValues method.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-0-1","dir":"Changelog","previous_headings":"","what":"Changes in 0.0.4","title":"MsBackendSql 0.0","text":"Add optional parameter tempfile.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-0-2","dir":"Changelog","previous_headings":"","what":"Changes in 0.0.3","title":"MsBackendSql 0.0","text":"Add peaksVariables methods add support parameter columns peaksData (Requires Spectra version 1.15.17).","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-0-3","dir":"Changelog","previous_headings":"","what":"Changes in 0.0.2","title":"MsBackendSql 0.0","text":"First full implementation MsBackendSql.","code":""}]
+[{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Storing Mass Spectrometry Data in SQL Databases","text":"Spectra Bioconductor package provides flexible expandable infrastructure Mass Spectrometry (MS) data. package supports interchangeable use different backends provide additional file support different ways store represent MS data. MsBackendSql package provides backends store data whole MS experiments SQL databases. data databases can easily (efficiently) accessed using Spectra objects use MsBackendSql class interface data database. Spectra objects minimal memory footprint hence allow analysis large data sets even computers limited hardware capabilities. certain operations, performance data representation superior low-memory (-disk) data representations Spectra’s MsBackendMzR backend. Finally, MsBackendSql supports also remote data access e.g. central database server hosting several large MS data sets.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Storing Mass Spectrometry Data in SQL Databases","text":"package can installed BiocManager package. install BiocManager use install.packages(\"BiocManager\") , , BiocManager::install(\"MsBackendSql\") install package.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"creating-and-using-msbackendsql-sql-databases","dir":"Articles","previous_headings":"","what":"Creating and using MsBackendSql SQL databases","title":"Storing Mass Spectrometry Data in SQL Databases","text":"MsBackendSql SQL databases can created either importing (raw) MS data MS data files using createMsBackendSqlDatabase() using backendInitialize() function providing addition database connection also full MS data import DataFrame. first example use createMsBackendSqlDatabase() function takes connection (empty) database names files data imported input parameters creates necessary database tables stores full data database. create empty SQLite database (temporary file) fill MS data two mzML files (msdata package). default m/z intensity values stored BLOB data types database. advantages performance extract peaks data database example allow filter peaks m/z values directly database. alternative also possible individual m/z intensity values separate rows database table. long table format results however considerably larger databases (potentially poorer performance). Note also code backend optimized MySQL/MariaDB databases taking advantage table partitioning specialized table storage options. SQL database server however also supported (also portable, self-contained SQLite databases). MsBackendSql package provides two backends interact databases: (default) MsBackendSql class MsBackendOfflineSql, inherits properties functions former, store connection database within object connects (disconnects) () database function call. allows use latter also parallel processing setups save/load object (e.g. using save saveRDS). Thus, applications MsBackendOfflineSql might used preferred backend SQL databases. access data database create Spectra object providing connection database constructor call specifying use MsBackendSql backend using source parameter. alternative, MsBackendOfflineSql backend also used interface MS data SQL database. contrast MsBackendSql, MsBackendOfflineSql contain active (open) connection database hence supports serializing (saving) object disk using e.g. save() function, parallel processing (supported database system). Thus, use cases MsBackendOfflineSql used instead MsBackendSql. See information MsBackendOfflineSql. Spectra objects allow also change backend backend (extending MsBackend) using setBackend() function. use function first load data memory changing MsBackendSql MsBackendMemory. function also possible change backend MsBackendSql case new database created data originating backend stored database. change backend MsBackendOfflineSql need provide connection information SQL database additional parameters. parameters need passed dbConnect() call establish connection database. parameters include database driver (parameter drv), database name eventually user name, host etc (see ?dbConnect information). simple example store data SQLite database thus need provide database name, corresponds SQLite database file. example store data temporary file. Similar Spectra object can retrieve available spectra variables using spectraVariables() function. MS peak data can accessed using either mz(), intensity() peaksData() functions. extract peaks matrix 5th spectrum display first 6 rows. data (peaks data spectra variables) always retrieved fly database resulting thus minimal memory footprint Spectra object. backend supports also adding additional spectra variables changing values. add 10 seconds retention time spectrum. operations however change data database (always considered read-) cached locally within backend object (memory). size memory object thus higher changing spectra variable. $<- operations can also used cache spectra variables (temporarily) memory can eventually improve performance. test time takes extract MS level spectrum database, cache MS levels memory using $msLevel <- test timing extract cached variable. can also use reset() function reset data original state (cause local spectra variables deleted backend initialized original data database). use MsBackendOfflineSql backend need provide information required connect database along database driver Spectra function. parameters required connect database depends SQL database used driver. example data stored SQLite database, hence use SQLite() database driver need provide database name dbname parameter. MySQL/MariaDB database use MariaDB() driver provide database name, user name, password well host name port database accessible. backend provides exact functionality MsBackendSql difference connection database opened closed function call. leads slightly lower performance, allows serialize object (.e. save/load object /disk) use (hence Spectra object) also parallel processing setup. contrast, MsBackendSql parallel processing disabled since possible share active backend connection within object across different parallel processes. compare performance two backends. performance difference result opening closing database connection call. Note also depend SQL server used. SQLite databases almost overhead.","code":"library(RSQLite)  dbfile <- tempfile() con <- dbConnect(SQLite(), dbfile)  library(MsBackendSql) fls <- dir(system.file(\"sciex\", package = \"msdata\"), full.names = TRUE) createMsBackendSqlDatabase(con, fls) sps <- Spectra(con, source = MsBackendSql()) sps ## MSn data (Spectra) with 1862 spectra in a MsBackendSql backend: ##        msLevel precursorMz  polarity ##      <integer>   <numeric> <integer> ## 1            1          NA         1 ## 2            1          NA         1 ## 3            1          NA         1 ## 4            1          NA         1 ## 5            1          NA         1 ## ...        ...         ...       ... ## 1858         1          NA         1 ## 1859         1          NA         1 ## 1860         1          NA         1 ## 1861         1          NA         1 ## 1862         1          NA         1 ##  ... 34 more variables/columns. ##  Use  'spectraVariables' to list all of them. ## Database: /tmp/Rtmp8LKjpZ/file7725e5d074d sps_mem <- setBackend(sps, MsBackendMemory()) sps_mem ## MSn data (Spectra) with 1862 spectra in a MsBackendMemory backend: ##        msLevel     rtime scanIndex ##      <integer> <numeric> <integer> ## 1            1     0.280         1 ## 2            1     0.559         2 ## 3            1     0.838         3 ## 4            1     1.117         4 ## 5            1     1.396         5 ## ...        ...       ...       ... ## 1858         1   258.636       927 ## 1859         1   258.915       928 ## 1860         1   259.194       929 ## 1861         1   259.473       930 ## 1862         1   259.752       931 ##  ... 34 more variables/columns. ## Processing: ##  Switch backend from MsBackendSql to MsBackendMemory [Sun Nov 17 16:34:32 2024] sps2 <- setBackend(sps_mem, MsBackendOfflineSql(), drv = SQLite(),                    dbname = tempfile()) sps2 ## MSn data (Spectra) with 1862 spectra in a MsBackendOfflineSql backend: ##        msLevel precursorMz  polarity ##      <integer>   <numeric> <integer> ## 1            1          NA         1 ## 2            1          NA         1 ## 3            1          NA         1 ## 4            1          NA         1 ## 5            1          NA         1 ## ...        ...         ...       ... ## 1858         1          NA         1 ## 1859         1          NA         1 ## 1860         1          NA         1 ## 1861         1          NA         1 ## 1862         1          NA         1 ##  ... 34 more variables/columns. ##  Use  'spectraVariables' to list all of them. ## Database: /tmp/Rtmp8LKjpZ/file772556f9c57e ## Processing: ##  Switch backend from MsBackendSql to MsBackendMemory [Sun Nov 17 16:34:32 2024] ##  Switch backend from MsBackendMemory to MsBackendOfflineSql [Sun Nov 17 16:34:33 2024] spectraVariables(sps) ##  [1] \"msLevel\"                  \"rtime\"                    ##  [3] \"acquisitionNum\"           \"scanIndex\"                ##  [5] \"dataStorage\"              \"dataOrigin\"               ##  [7] \"centroided\"               \"smoothed\"                 ##  [9] \"polarity\"                 \"precScanNum\"              ## [11] \"precursorMz\"              \"precursorIntensity\"       ## [13] \"precursorCharge\"          \"collisionEnergy\"          ## [15] \"isolationWindowLowerMz\"   \"isolationWindowTargetMz\"  ## [17] \"isolationWindowUpperMz\"   \"peaksCount\"               ## [19] \"totIonCurrent\"            \"basePeakMZ\"               ## [21] \"basePeakIntensity\"        \"ionisationEnergy\"         ## [23] \"lowMZ\"                    \"highMZ\"                   ## [25] \"mergedScan\"               \"mergedResultScanNum\"      ## [27] \"mergedResultStartScanNum\" \"mergedResultEndScanNum\"   ## [29] \"injectionTime\"            \"filterString\"             ## [31] \"spectrumId\"               \"ionMobilityDriftTime\"     ## [33] \"scanWindowLowerLimit\"     \"scanWindowUpperLimit\"     ## [35] \"spectrum_id_\" peaksData(sps)[[5]] |> head() ##            mz intensity ## [1,] 105.0347         0 ## [2,] 105.0362       164 ## [3,] 105.0376         0 ## [4,] 105.0391         0 ## [5,] 105.0405       328 ## [6,] 105.0420         0 print(object.size(sps), units = \"KB\") ## 91.5 Kb sps$rtime <- sps$rtime + 10 print(object.size(sps), units = \"KB\") ## 106.2 Kb system.time(msLevel(sps)) ##    user  system elapsed  ##   0.007   0.000   0.007 sps$msLevel <- msLevel(sps) system.time(msLevel(sps)) ##    user  system elapsed  ##   0.002   0.000   0.003 sps <- reset(sps) sps_off <- Spectra(dbfile, drv = SQLite(),                    source = MsBackendOfflineSql()) sps_off ## MSn data (Spectra) with 1862 spectra in a MsBackendOfflineSql backend: ##        msLevel precursorMz  polarity ##      <integer>   <numeric> <integer> ## 1            1          NA         1 ## 2            1          NA         1 ## 3            1          NA         1 ## 4            1          NA         1 ## 5            1          NA         1 ## ...        ...         ...       ... ## 1858         1          NA         1 ## 1859         1          NA         1 ## 1860         1          NA         1 ## 1861         1          NA         1 ## 1862         1          NA         1 ##  ... 34 more variables/columns. ##  Use  'spectraVariables' to list all of them. ## Database: /tmp/Rtmp8LKjpZ/file7725e5d074d library(microbenchmark) microbenchmark(msLevel(sps), msLevel(sps_off)) ## Unit: milliseconds ##              expr      min       lq     mean   median       uq      max neval ##      msLevel(sps) 5.318853 5.582285 5.776706 5.666632 5.802756 10.35720   100 ##  msLevel(sps_off) 6.942943 7.330998 7.620031 7.530921 7.715440 12.08204   100"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"performance-comparison-with-other-backends","dir":"Articles","previous_headings":"","what":"Performance comparison with other backends","title":"Storing Mass Spectrometry Data in SQL Databases","text":"need retrieve spectra data --fly database impact performance data access function Spectra objects using MsBackendSql backends. evaluate impact next compare performance MsBackendSql Spectra backends, specifically, MsBackendMzR default backend read represent raw MS data, MsBackendMemory backend keeps MS data memory (thus suggested larger MS experiments). Similar MsBackendMzR, also MsBackendSql keeps limited amount data memory. -disk backends need thus retrieve spectra MS peaks data --fly either original raw data files (case MsBackendMzR) SQL database (case MsBackendSql). -memory backend MsBackendMemory supposed provide fastest data access since data kept memory. thus create Spectra objects data using different backends. first compare memory footprint 3 backends. MsBackendSql lowest memory footprint 3 backends keep data memory. MsBackendMzR keeps spectra variables, except MS peaks data, memory thus larger size. MsBackendMemory keeps data (including MS peaks data) memory thus largest size memory. Next compare performance extract MS level spectrum 4 different Spectra objects. Extracting MS levels thus slowest MsBackendSql, surprising backends keep data memory MsBackendSql needs retrieve database. next compare performance access full peaks data Spectra object. expected, MsBackendMemory fasted access full peaks data. MsBackendSql outperforms however MsBackendMzR providing faster access m/z intensity values. Performance can improved MsBackendMzR using parallel processing. Note MsBackendSql support parallel processing thus parallel processing (silently) disabled functions peaksData(). next compare performance subsetting operations. two -disk backends MsBackendSql MsBackendMzR show comparable performance operation. filtering involves access spectra variables (retention time case) , MsBackendSql needs first retrieved backend. MsBackendSql backend allows however also cache spectra variables (.e. stored within MsBackendSql object). access cached spectra variables can eventually faster dedicated SQL query needed. evaluate performance pure subsetting operation first define indices 10 random spectra subset Spectra objects . MsBackendSql outperforms backends keep data memory hence need subset . two backends need subset data keep memory cases data frame either reduced set spectra variables full MS data. last compare also extraction peaks data subset Spectra objects. MsBackendSql outperforms MsBackendMzR , unexpectedly, MsBackendMemory provides fasted access.","code":"sps <- Spectra(con, source = MsBackendSql()) sps_mzr <- Spectra(fls, source = MsBackendMzR()) sps_im <- setBackend(sps_mzr, backend = MsBackendMemory()) print(object.size(sps), units = \"KB\") ## 91.5 Kb print(object.size(sps_mzr), units = \"KB\") ## 386.7 Kb print(object.size(sps_im), units = \"KB\") ## 54494.5 Kb library(microbenchmark) microbenchmark(msLevel(sps),                msLevel(sps_mzr),                msLevel(sps_im)) ## Unit: microseconds ##              expr      min       lq       mean   median        uq      max ##      msLevel(sps) 5307.963 5531.631 5855.78739 5777.007 6070.2650 9645.986 ##  msLevel(sps_mzr)  369.430  391.065  406.52328  405.011  416.6575  642.689 ##   msLevel(sps_im)   10.861   13.776   22.43835   20.348   27.7165   65.723 ##  neval ##    100 ##    100 ##    100 microbenchmark(peaksData(sps, BPPARAM = SerialParam()),                peaksData(sps_mzr, BPPARAM = SerialParam()),                peaksData(sps_im, BPPARAM = SerialParam()), times = 10) ## Unit: microseconds ##                                         expr        min         lq       mean ##      peaksData(sps, BPPARAM = SerialParam())  99135.484 125869.681 237565.851 ##  peaksData(sps_mzr, BPPARAM = SerialParam()) 437705.436 455328.668 631429.534 ##   peaksData(sps_im, BPPARAM = SerialParam())    307.164    348.019   1905.919 ##       median         uq       max neval ##  129195.3065 376300.534  564061.9    10 ##  480673.1690 708454.956 1184310.8    10 ##     539.9725    665.401   14498.5    10 m2 <- MulticoreParam(2) microbenchmark(peaksData(sps, BPPARAM = m2),                peaksData(sps_mzr, BPPARAM = m2),                peaksData(sps_im, BPPARAM = m2), times = 10) ## Unit: microseconds ##                              expr        min         lq        mean    median ##      peaksData(sps, BPPARAM = m2) 103799.987 110091.265 121073.2584 124252.54 ##  peaksData(sps_mzr, BPPARAM = m2) 446914.127 479684.756 695696.4720 532158.70 ##   peaksData(sps_im, BPPARAM = m2)    306.402    622.722    607.9765    648.45 ##          uq         max neval ##  129857.883  133608.220    10 ##  862147.247 1192024.219    10 ##     700.147     806.245    10 microbenchmark(filterRt(sps, rt = c(50, 100)),                filterRt(sps_mzr, rt = c(50, 100)),                filterRt(sps_im, rt = c(50, 100))) ## Unit: microseconds ##                                expr      min       lq      mean    median ##      filterRt(sps, rt = c(50, 100)) 2622.873 2706.966 3027.5222 2795.5560 ##  filterRt(sps_mzr, rt = c(50, 100)) 2015.090 2126.502 2345.2143 2251.5955 ##   filterRt(sps_im, rt = c(50, 100))  441.944  482.270  528.7807  523.4665 ##        uq       max neval ##  2913.697 19829.285   100 ##  2433.660  7559.725   100 ##   550.512   901.602   100 idx <- sample(seq_along(sps), 10) microbenchmark(sps[idx],                sps_mzr[idx],                sps_im[idx]) ## Unit: microseconds ##          expr     min       lq     mean   median       uq      max neval ##      sps[idx] 131.346 137.7065 149.3402 147.8110 153.1410  275.354   100 ##  sps_mzr[idx] 633.662 646.4010 671.5505 656.3600 674.0125 1525.096   100 ##   sps_im[idx] 225.120 231.8025 241.7284 237.3625 245.5230  401.359   100 sps_10 <- sps[idx] sps_mzr_10 <- sps_mzr[idx] sps_im_10 <- sps_im[idx]  microbenchmark(peaksData(sps_10),                peaksData(sps_mzr_10),                peaksData(sps_im_10),                times = 10) ## Unit: microseconds ##                   expr       min        lq       mean    median        uq ##      peaksData(sps_10)  2624.136  2776.300  3438.1887  3754.535  3959.327 ##  peaksData(sps_mzr_10) 74668.808 76957.188 77493.6373 77753.818 78581.648 ##   peaksData(sps_im_10)   359.410   389.236   471.2794   442.415   568.882 ##        max neval ##   4076.656    10 ##  78690.992    10 ##    608.756    10"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"considerations-for-database-systemsservers","dir":"Articles","previous_headings":"Performance comparison with other backends","what":"Considerations for database systems/servers","title":"Storing Mass Spectrometry Data in SQL Databases","text":"backends MsBackendSql package use standard SQL calls retrieve MS data database hence SQL database system (R package available) supported. SQLite-based databases represent easiest user friendly solution since database server administration user management required. Indeed, performance SQLite high, even large data sets. Server-based databases hand advantage enable centralized storage control MS data (inclusive user management etc). Also, server systems also allow data set server-specific configurations improve performance. comparison SQLite-based MariaDB-based MsBackendSql database large data set comprising 8,000 samples 15,000,000 spectra available . brief, performance extract data comparable individual spectra variables even faster SQLite database. complex SQL queries involved (combining several primary keys data fields) advanced MariaDB database outperformed SQLite.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"other-properties-of-the-msbackendsql","dir":"Articles","previous_headings":"","what":"Other properties of the MsBackendSql","title":"Storing Mass Spectrometry Data in SQL Databases","text":"MsBackendSql backend support parallel processing since database connection can shared across different (parallel) processes. Thus, methods Spectra objects use MsBackendSql automatically (silently) disable parallel processing even dedicated parallel processing setup passed along BPPARAM method. functions Spectra objects require load MS peak data (.e., m/z intensity values) memory. large data sets (computers limited hardware resources) function calls can cause --memory errors. One example lengths() function determines number peaks per spectrum loading peak matrix first memory. functions ideally called using peaksapply() function parameter chunkSize (e.g., peaksapply(sps, lengths, chunkSize = 5000L)). Instead processing full data set, data first split chunks size chunkSize stepwise processed. Hence, data chunkSize spectra loaded memory one iteration.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Storing Mass Spectrometry Data in SQL Databases","text":"MsBackendSql provides MS data representations storage mode minimal memory footprint (R) still comparably efficient standard processing subsetting operations. backend specifically useful large MS data sets, even hosted remote (MySQL/MariaDB) servers. potential use case backend thus set central storage place MS experiments data analysts connecting remotely server perform initial data exploration filtering. subsetting smaller data set interest, users retrieve/download data changing backend e.g. MsBackendMemory, result download full data user computer’s memory.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.html","id":"session-information","dir":"Articles","previous_headings":"","what":"Session information","title":"Storing Mass Spectrometry Data in SQL Databases","text":"","code":"sessionInfo() ## R Under development (unstable) (2024-11-13 r87330) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 24.04.1 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0 ##  ## locale: ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C             ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats4    stats     graphics  grDevices utils     datasets  methods   ## [8] base      ##  ## other attached packages: ## [1] microbenchmark_1.5.0 RSQLite_2.3.7        MsBackendSql_1.7.0   ## [4] Spectra_1.17.0       BiocParallel_1.41.0  S4Vectors_0.45.2     ## [7] BiocGenerics_0.53.3  generics_0.1.3       BiocStyle_2.35.0     ##  ## loaded via a namespace (and not attached): ##  [1] sass_0.4.9             MsCoreUtils_1.19.0     hms_1.1.3              ##  [4] digest_0.6.37          evaluate_1.0.1         bookdown_0.41          ##  [7] fastmap_1.2.0          blob_1.2.4             jsonlite_1.8.9         ## [10] ProtGenerics_1.39.0    progress_1.2.3         mzR_2.41.0             ## [13] DBI_1.2.3              BiocManager_1.30.25    codetools_0.2-20       ## [16] textshaping_0.4.0      jquerylib_0.1.4        cli_3.6.3              ## [19] rlang_1.1.4            crayon_1.5.3           Biobase_2.67.0         ## [22] bit64_4.5.2            cachem_1.1.0           yaml_2.3.10            ## [25] tools_4.5.0            parallel_4.5.0         memoise_2.0.1          ## [28] ncdf4_1.23             vctrs_0.6.5            R6_2.5.1               ## [31] lifecycle_1.0.4        fs_1.6.5               htmlwidgets_1.6.4      ## [34] IRanges_2.41.1         bit_4.5.0              clue_0.3-66            ## [37] MASS_7.3-61            ragg_1.3.3             cluster_2.1.6          ## [40] pkgconfig_2.0.3        desc_1.4.3             pkgdown_2.1.1.9000     ## [43] bslib_0.8.0            Rcpp_1.0.13-1          data.table_1.16.2      ## [46] systemfonts_1.1.0      xfun_0.49              knitr_1.49             ## [49] htmltools_0.5.8.1      rmarkdown_2.29         compiler_4.5.0         ## [52] prettyunits_1.2.0      MetaboCoreUtils_1.15.0"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Rainer. Author, maintainer. Chong Tang. Contributor. Laurent Gatto. Contributor.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Rainer J (2024). MsBackendSql: SQL-based Mass Spectrometry Data Backend. R package version 1.7.0, https://github.com/RforMassSpectrometry/MsBackendSql.","code":"@Manual{,   title = {MsBackendSql: SQL-based Mass Spectrometry Data Backend},   author = {Johannes Rainer},   year = {2024},   note = {R package version 1.7.0},   url = {https://github.com/RforMassSpectrometry/MsBackendSql}, }"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"sql-based-mass-spectrometry-data-backend","dir":"","previous_headings":"","what":"SQL-based Mass Spectrometry Data Backend","title":"SQL-based Mass Spectrometry Data Backend","text":"repository provides backend Spectra objects supports storage mass spectrometry (MS) data SQL database. package provides functionality create databases original (raw) MS data files (mzML, mzXML netCDF format) allows extract data efficient way. information see package homepage.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"creating-a-database","dir":"","previous_headings":"","what":"Creating a database","title":"SQL-based Mass Spectrometry Data Backend","text":"providing connection SQL database, createMsBackendSqlDatabase imports raw MS data provided file names stores dedicated database tables created import. MsBackendSql supports type SQL database, currently optimized MySQL/MariaDB databases.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"using-a-msbackendsql-database","dir":"","previous_headings":"","what":"Using a MsBackendSql database","title":"SQL-based Mass Spectrometry Data Backend","text":"MS data MsBackendSql database can accessed Spectra package using MsBackendSql MS backend. Assuming variable dbcon represents (RDBI) database connection MsBackendSql, data can represented/used Spectra object : information see package homepage.","code":"library(Spectra) library(MsBackendSql) sps <- Spectra(dbcon, source = MsBackendSql())"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"SQL-based Mass Spectrometry Data Backend","text":"package can installed ","code":"install.packages(\"BiocManager\") BiocManager::install(\"MsBackendSql\")"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/index.html","id":"contributions","dir":"","previous_headings":"","what":"Contributions","title":"SQL-based Mass Spectrometry Data Backend","text":"Contributions highly welcome follow contribution guidelines. Also, please check coding style guidelines RforMassSpectrometry vignette.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":null,"dir":"Reference","previous_headings":"","what":"SQL-based MS backend without active database connection — MsBackendOfflineSql","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"MsBackendOfflineSql backend extends MsBackendSql() backend directly inherits thus functions well properties. difference two backend MsBackendSql keeps active connection SQL database inside object MsBackendOfflineSql backends reconnects SQL database query. performance latter slightly lower (due need connect/disconnect database function call) can also used parallel processing environment.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"","code":"MsBackendOfflineSql()  # S4 method for class 'MsBackendOfflineSql' backendInitialize(   object,   drv = NULL,   dbname = character(),   user = character(),   password = character(),   host = character(),   port = NA_integer_,   data,   ... )"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"object MsBackendOfflineSql object. drv DBI database driver object (SQLite() RSQLite package MariaDB() RMariaDB package). See dbConnect() information. dbname character(1) name database. Passed directly dbConnect(). user character(1) user name database. Passed directly dbConnect(). password character(1) password database. Note password stored (unencrypted) within object. Passed directly dbConnect(). host character(1) host running database. Passed directly dbConnect(). port integer(1) port number (optional). Passed directly dbConnect(). data backendInitialize(): optional DataFrame full spectra data inserted (new) MsBackendSql database. provided, assumed provided database connection information (writeable) empty database data inserted. data output spectraData another backend. ... ignored.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":"creation-of-backend-objects","dir":"Reference","previous_headings":"","what":"Creation of backend objects","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"empty instance MsBackendOfflineSql class can created using MsBackendOfflineSql() function. existing MsBackendSql SQL database can loaded backendInitialize() function. function takes parameters drv, dbname, user, password, host port, parameters passed dbConnect() function connect (existing) SQL database. See MsBackendSql() information create MsBackend SQL database.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendOfflineSql.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"SQL-based MS backend without active database connection — MsBackendOfflineSql","text":"Johannes Rainer","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":null,"dir":"Reference","previous_headings":"","what":"Spectra MS backend storing data in a SQL database — MsBackendSql","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"MsBackendSql implementation MsBackend() class Spectra() objects stores retrieves MS data SQL database. New databases can created raw MS data files using createMsBackendSqlDatabase().","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"","code":"MsBackendSql()  createMsBackendSqlDatabase(   dbcon,   x = character(),   backend = MsBackendMzR(),   chunksize = 10L,   blob = TRUE,   partitionBy = c(\"none\", \"spectrum\", \"chunk\"),   partitionNumber = 10L )  # S4 method for class 'MsBackendSql' show(object)  # S4 method for class 'MsBackendSql' backendInitialize(object, dbcon, data, ...)  # S4 method for class 'MsBackendSql' dataStorage(object)  # S4 method for class 'MsBackendSql' x[i, j, ..., drop = FALSE]  # S4 method for class 'MsBackendSql,ANY' extractByIndex(object, i)  # S4 method for class 'MsBackendSql' peaksData(object, columns = c(\"mz\", \"intensity\"))  # S4 method for class 'MsBackendSql' peaksVariables(object)  # S4 method for class 'MsBackendSql' intensity(object) <- value  # S4 method for class 'MsBackendSql' mz(object) <- value  # S4 method for class 'MsBackendSql' x$name <- value  # S4 method for class 'MsBackendSql' spectraData(object, columns = spectraVariables(object))  # S4 method for class 'MsBackendSql' reset(object)  # S4 method for class 'MsBackendSql' spectraNames(object)  # S4 method for class 'MsBackendSql' spectraNames(object) <- value  # S4 method for class 'MsBackendSql' filterMsLevel(object, msLevel = uniqueMsLevels(object))  # S4 method for class 'MsBackendSql' filterRt(object, rt = numeric(), msLevel. = integer())  # S4 method for class 'MsBackendSql' filterDataOrigin(object, dataOrigin = character())  # S4 method for class 'MsBackendSql' filterPrecursorMzRange(object, mz = numeric())  # S4 method for class 'MsBackendSql' filterPrecursorMzValues(object, mz = numeric(), ppm = 20, tolerance = 0)  # S4 method for class 'MsBackendSql' uniqueMsLevels(object, ...)  # S4 method for class 'MsBackendSql' backendMerge(object, ...)  # S4 method for class 'MsBackendSql' precScanNum(object)  # S4 method for class 'MsBackendSql' centroided(object)  # S4 method for class 'MsBackendSql' smoothed(object)  # S4 method for class 'MsBackendSql' tic(object, initial = TRUE)  # S4 method for class 'MsBackendSql' supportsSetBackend(object, ...)  # S4 method for class 'MsBackendSql' backendBpparam(object, BPPARAM = bpparam())  # S4 method for class 'MsBackendSql' dbconn(x)"},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"dbcon Connection database. x createMsBackendSqlDatabase(): character names raw data files data imported. methods MsqlBackend instance. backend createMsBackendSqlDatabase(): MS backend can used import MS data raw files specified parameter x. chunksize createMsBackendSqlDatabase(): integer(1) defining number input processed per iteration. chunksize = 1 file specified x imported data inserted database. chunksize = 5 data 5 files imported (parallel) inserted database. Thus, higher values might result faster database creation, require also memory. blob createMsBackendSqlDatabase(): logical(1) whether individual m/z intensity values stored separately (blob = FALSE) m/z intensity values spectrum stored single BLOB SQL data type (blob = TRUE, default). partitionBy createMsBackendSqlDatabase(): character(1) defining peak data table partitioned. \"none\" (default): partitioning, \"spectrum\": peaks assigned partition based spectrum ID (number), .e. spectra evenly (consecutively) assigned across partitions. partitionNumber = 3, first spectrum assigned first partition, second second, third third fourth spectrum first partition. \"chunk\": spectra processed part chunk placed partition. spectra next processed chunk assigned next partition. Note available MySQL/MariaDB databases, .e., con MariaDBConnection. See details information. partitionNumber createMsBackendSqlDatabase(): integer(1) defining number partitions database table partitioned (supported MySQL/MariaDB databases). object MsBackendSql instance. data backendInitialize(): optional DataFrame full spectra data inserted (new) MsBackendSql database. provided, assumed dbcon (writeable) connection empty database data inserted. data output spectraData another backend. ... [: ignored. backendInitialize, parameter data used: additional parameters passed function creating database blob. [: integer logical subset object. j [: ignored. drop [: logical(1), ignored. columns spectraData(): character() optionally defining subset spectra variables returned. Defaults columns = spectraVariables(object) hence variables returned. peaksData accessor: optional character requested columns individual matrix returned list. Defaults columns = c(\"mz\", \"intensity\") columns listed peaksVariables supported. value setter methods: replacement value. name <-: character(1) name spectra variable replace. msLevel filterMsLevel(): integer specifying MS levels filter data. rt filterRt(): numeric(2) lower upper retention time. Spectra retention time >= rt[1] <= rt[2] returned. msLevel. filterRt(): integerwith MS level(s) retention time filter applied (spectra MS levels considered filter returned **). specified, retention time filter applied MS levels inobject`. dataOrigin filterDataOrigin(): character data origin values data subsetted. mz filterPrecursorMzRange(): numeric(2) desired lower upper limit precursor m/z range. filterPrecursorMzValues(): numeric m/z value(s) filter object. ppm filterPrecursorMzValues(): numeric m/z-relative maximal acceptable difference m/z value considered matching. Can length 1 equal length(mz). tolerance filterPrecursorMzValues(): numeric absolute difference m/z values considered matching. Can length 1 equal length(mz). initial tic(): logical(1) whether original total ion count returned (initial = TRUE, default) whether calculated spectras' intensities (initial = FALSE). BPPARAM backendBpparam(): BiocParallel parallel processing setup. See bpparam() information.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"See documentation respective function.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"MsBackendSql class principally read-backend extending MsBackendCached() backend Spectra package allows changing adding (temporarily) spectra variables without changing original data SQL database.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"MsBackendSql backend keeps (open) connection SQL database data hence support saving/loading backend disk (e.g. using save saveRDS). Also, reason, MsBackendSql support parallel processing. backendBpparam() method MsBackendSql thus always return SerialParam() object. MsBackendOfflineSql() used alternative supports saving/loading data /disk supports also parallel processing.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"creation-of-backend-objects","dir":"Reference","previous_headings":"","what":"Creation of backend objects","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"New backend objects can created MsBackendSql() function. SQL databases can created filled MS data raw data files using createMsBackendSqlDatabase() function using backendInitialize() providing data parameter data. addition possible create database Spectra object changing backend MsBackendSql MsBackendOfflineSql using setBackend() function. Existing SQL databases (created previously createMsBackendSqlDatabase() backendInitialize() data parameter) can loaded using conventional way create/initialize MsBackend classes, .e. using backendInitialize(). createMsBackendSqlDatabase(): create database fill MS data. Parameter dbcon expected database connection, parameter x character vector file names import data. Parameter backend used actual data import defaults backend = MsBackendMzR() hence allowing import data mzML, mzXML netCDF files. Parameter chunksize allows define number files (x) data imported one iteration. default chunksize = 10L data imported 10 files x time (backend supports even parallel) data inserted database. Larger chunk sizes require memory also larger disk space (data import performed temporary files) might eventually faster. Parameter blob allows define whether m/z intensity values spectrum stored BLOB SQL data type database (blob = TRUE, default) individual m/z intensity values peak stored separately (blob = FALSE). latter case results much larger database slower performance peaksData function, allow define custom (manual) SQL queries individual peak values. data can stored SQL database, present suggested use MySQL/MariaDB databases. dbcon connection MySQL/MariaDB database, tables use ARIA engine providing faster data access use table partitioning: tables splitted multiple partitions can improve data insertion index generation. Partitioning can defined parameters partitionBy partitionNumber. default partitionBy = \"none\" partitioning performed. blob = TRUE partitioning usually required. blob = FALSE  large datasets suggested enable table partitioning selecting either partitionBy = \"spectrum\" partitionBy = \"chunk\". first option assignes consecutive spectra different partitions latter puts spectra files part chunk partition. options performance partitionBy = \"spectrum\" requires less disk space. Note , inserting data takes considerable amount time, also subsequent creation database indices can take long (even longer data insertion blob = FALSE). backendInitialize(): get access initialize MsBackendSql object. Parameter object supposed MsBackendSql instance, created e.g. MsBackendSql(). Parameter dbcon expected connection existing MsBackendSql SQL database (created e.g. createMsBackendSqlDatabase()). backendInitialize() can alternatively also used create new MsBackendSql database using optional data parameter. case, dbcon expected writeable connection empty database data DataFrame full spectra data inserted database. format data match format DataFrame returned spectraData() function requires columns \"mz\" \"intensity\" m/z intensity values spectrum. backendInitialize() call create necessary tables database, fill tables provided data return MsBackendSql database. Thus, MsBackendSql supports setBackend method Spectra change () backend MsBackendSql. Note however chunk-wise (parallel) processing needs disabled case passing eventually f = factor() setBackend() call. supportsSetBackend(): whether MsBackendSql supports setBackend() method change MsBackend Spectra object MsBackendSql. Returns TRUE, thus, changing backend MsBackendSql supported writeable database connection provided addition parameter dbcon (.e. setBackend(sps, MsBackendSql(), dbcon = con) con connection empty database store full spectra data Spectra object sps specified database return Spectra object uses MsBackendSql). backendBpparam(): whether MsBackendSql supports parallel processing. Takes MsBackendSql parallel processing setup (see bpparam() details) input always returns SerialParam() since MsBackendSql support parallel processing. dbconn(): returns connection database.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"subsetting-merging-and-filtering-data","dir":"Reference","previous_headings":"","what":"Subsetting, merging and filtering data","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"MsBackendSql objects can subsetted using [ extractByIndex() functions. Internally, simply subset integer vector primary keys eventually cached data. original data database affected subsetting operation. subsetting operation can undone resetting object reset() function. Subsetting arbitrary order well index replication supported. Multiple MsBackendSql objects can also merged (combined) backendMerge() function. Note requires MsBackendSql objects connected database. function thus mostly used combining MsBackendSql objects previously splitted using e.g. split(). addition, MsBackendSql supports filtering methods available MsBackendCached(). Implementation filter functions optimized MsBackendSql objects : filterDataOrigin(): filter object retaining spectra dataOrigin spectra variable values matching provided ones parameter dataOrigin. function returns results order values provided parameter dataOrigin. filterMsLevel(): filter object based MS levels specified parameter msLevel. function filtering using SQL queries. \"msLevel\" local variable stored within object (hence memory) default implementation MsBackendCached used instead. filterPrecursorMzRange(): filters data keeping spectra precursorMz within m/z value range provided parameter mz (.e. spectra precursor m/z >= mz[1L] <= mz[2L]). filterPrecursorMzValues(): filters data keeping spectra precursor m/z values matching value(s) provided parameter mz. Parameters ppmandtoleranceallow specify acceptable differences compared values. Lengths ofppmandtolerancecan either1or equal tolength(mz)` use different values ppm tolerance provided m/z value. filterRt(): filter object keeping spectra retention times within specified retention time range (parameter rt). Optional parameter msLevel. allows restrict retention time filter provided MS level(s) returning spectra MS levels.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"accessing-and-modifying-data","dir":"Reference","previous_headings":"","what":"Accessing and modifying data","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"functions listed specifically implemented MsBackendSql. addition, MsBackendSql inherits supports data accessor, filtering functions data manipulation functions MsBackendCached(). $, $<-: access set (add) spectra variables object. Spectra variables added modified using $<- cached locally within object (data database never changed). restore object (.e. drop cached values) reset function can used. dataStorage(): returns character vector length spectra object name database containing data. intensity<-: supported. mz<-: supported. peaksData(): returns list spectras' peak data. length list equal number spectra object. element list matrix columns according parameter columns. empty spectrum, matrix 0 rows returned. Use peaksVariables(object) list supported values parameter columns. peaksVariables(): returns character available peak variables, .e. columns queried peaksData(). reset(): restores MsBackendSql re-initializing data database. subsetting cached spectra variables lost. spectraData(): gets general spectrum metadata. spectraData() returns DataFrame number rows spectra object. Parameter columns allows select specific spectra variables. spectraNames(), spectraNames<-: returns character length equal number spectra object primary keys spectra database (converted character). Replacing spectra names spectraNames<- supported. uniqueMsLevels(): returns unique MS levels spectra object. tic(): returns originally reported total ion count (initial = TRUE) calculates total ion count intensities spectrum (initial = FALSE).","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"implementation-notes","dir":"Reference","previous_headings":"","what":"Implementation notes","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"Internally, MsBackendSql class contains primary keys spectra stored SQL database. Keeping integer memory guarantees minimal memory footpring object. Still, depending number spectra database, integer vector might become large. data access involve SQL calls retrieve data database. extending MsBackendCached() object Spectra package, MsBackendSql supports (temporarily, .e. duration R session) add modify spectra variables. however stored data.frame within object thus increasing memory demand object.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"Johannes Rainer","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/reference/MsBackendSql.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spectra MS backend storing data in a SQL database — MsBackendSql","text":"","code":"#### ## Create a new MsBackendSql database  ## Define a file from which to import the data data_file <- system.file(\"microtofq\", \"MM8.mzML\", package = \"msdata\")  ## Create a database/connection to a database library(RSQLite) db_file <- tempfile() dbc <- dbConnect(SQLite(), db_file)  ## Import the data from the file into the database createMsBackendSqlDatabase(dbc, data_file) #> Importing data ...  #>  #> [==========================================================] 1/1 (100%) in  1s #>  #> Creating indices  #> . #> . #> . #> . #>  Done #> [1] TRUE dbDisconnect(dbc)  ## Initialize a MsBackendSql dbc <- dbConnect(SQLite(), db_file) be <- backendInitialize(MsBackendSql(), dbc)  be #> MsBackendSql with 198 spectra #>       msLevel precursorMz  polarity #>     <integer>   <numeric> <integer> #> 1           1          NA         1 #> 2           1          NA         1 #> 3           1          NA         1 #> 4           1          NA         1 #> 5           1          NA         1 #> ...       ...         ...       ... #> 194         1          NA         1 #> 195         1          NA         1 #> 196         1          NA         1 #> 197         1          NA         1 #> 198         1          NA         1 #>  ... 34 more variables/columns. #>  Use  'spectraVariables' to list all of them. #> Database: /tmp/RtmpjVGmuK/file76664c5f5a0f  ## Original data source head(be$dataOrigin) #> [1] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [2] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [3] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [4] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [5] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\" #> [6] \"/__w/_temp/Library/msdata/microtofq/MM8.mzML\"  ## Data storage head(dataStorage(be)) #> [1] \"/tmp/RtmpjVGmuK/file76664c5f5a0f\" \"/tmp/RtmpjVGmuK/file76664c5f5a0f\" #> [3] \"/tmp/RtmpjVGmuK/file76664c5f5a0f\" \"/tmp/RtmpjVGmuK/file76664c5f5a0f\" #> [5] \"/tmp/RtmpjVGmuK/file76664c5f5a0f\" \"/tmp/RtmpjVGmuK/file76664c5f5a0f\"  ## Access all spectra data spd <- spectraData(be) spd #> DataFrame with 198 rows and 37 columns #>       msLevel     rtime acquisitionNum scanIndex                             mz #>     <integer> <numeric>      <integer> <integer>                  <NumericList> #> 1           1     0.486              1         1    104.554,106.996,107.966,... #> 2           1     0.822              2         2    107.960,109.964,112.027,... #> 3           1     1.159              3         3    107.963,112.021,113.035,... #> 4           1     1.495              4         4    105.971,109.984,112.028,... #> 5           1     1.832              5         5    104.474,107.000,109.968,... #> ...       ...       ...            ...       ...                            ... #> 194         1   65.4360            194       194    106.992,111.459,112.022,... #> 195         1   65.7720            195       195  99.0797,109.0031,112.0232,... #> 196         1   66.1092            196       196    102.927,108.970,112.028,... #> 197         1   66.4458            197       197    111.058,112.026,113.029,... #> 198         1   66.7818            198       198    111.044,112.024,112.518,... #>           intensity            dataStorage             dataOrigin centroided #>       <NumericList>            <character>            <character>  <logical> #> 1      23,35,50,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #> 2    35, 24,140,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #> 3    28,179,350,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #> 4    25, 28,131,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #> 5      26,30,25,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #> ...             ...                    ...                    ...        ... #> 194    34,24,86,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #> 195  24, 22,198,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #> 196    29,22,98,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #> 197  31,124,189,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #> 198    67,84,22,... /tmp/RtmpjVGmuK/file.. /__w/_temp/Library/m..       TRUE #>      smoothed  polarity precScanNum precursorMz precursorIntensity #>     <logical> <integer>   <integer>   <numeric>          <numeric> #> 1          NA         1          NA          NA                 NA #> 2          NA         1          NA          NA                 NA #> 3          NA         1          NA          NA                 NA #> 4          NA         1          NA          NA                 NA #> 5          NA         1          NA          NA                 NA #> ...       ...       ...         ...         ...                ... #> 194        NA         1          NA          NA                 NA #> 195        NA         1          NA          NA                 NA #> 196        NA         1          NA          NA                 NA #> 197        NA         1          NA          NA                 NA #> 198        NA         1          NA          NA                 NA #>     precursorCharge collisionEnergy isolationWindowLowerMz #>           <integer>       <numeric>              <numeric> #> 1                NA              NA                     NA #> 2                NA              NA                     NA #> 3                NA              NA                     NA #> 4                NA              NA                     NA #> 5                NA              NA                     NA #> ...             ...             ...                    ... #> 194              NA              NA                     NA #> 195              NA              NA                     NA #> 196              NA              NA                     NA #> 197              NA              NA                     NA #> 198              NA              NA                     NA #>     isolationWindowTargetMz isolationWindowUpperMz peaksCount totIonCurrent #>                   <numeric>              <numeric>  <integer>     <numeric> #> 1                        NA                     NA       1743         97322 #> 2                        NA                     NA       1708         98590 #> 3                        NA                     NA       1708         96425 #> 4                        NA                     NA       1747         97144 #> 5                        NA                     NA       1730         94631 #> ...                     ...                    ...        ...           ... #> 194                      NA                     NA       2267        142472 #> 195                      NA                     NA       2488        167102 #> 196                      NA                     NA       2324        137565 #> 197                      NA                     NA       2105        113086 #> 198                      NA                     NA       1996         97257 #>     basePeakMZ basePeakIntensity ionisationEnergy     lowMZ    highMZ #>      <numeric>         <numeric>        <numeric> <numeric> <numeric> #> 1      144.050              7250                0   104.554  1004.470 #> 2      144.050              7064                0   107.960  1002.799 #> 3      144.050              7124                0   107.963   993.959 #> 4      144.051              7067                0   105.971   986.756 #> 5      144.051              6891                0   104.474  1003.469 #> ...        ...               ...              ...       ...       ... #> 194    144.051              4615                0  106.9921  1003.828 #> 195    144.051              3812                0   99.0797  1003.270 #> 196    144.050              3526                0  102.9272  1000.594 #> 197    144.050              3902                0  111.0582   984.228 #> 198    144.051              3587                0  111.0437  1000.851 #>     mergedScan mergedResultScanNum mergedResultStartScanNum #>      <integer>           <integer>                <integer> #> 1           NA                  NA                       NA #> 2           NA                  NA                       NA #> 3           NA                  NA                       NA #> 4           NA                  NA                       NA #> 5           NA                  NA                       NA #> ...        ...                 ...                      ... #> 194         NA                  NA                       NA #> 195         NA                  NA                       NA #> 196         NA                  NA                       NA #> 197         NA                  NA                       NA #> 198         NA                  NA                       NA #>     mergedResultEndScanNum injectionTime filterString  spectrumId #>                  <integer>     <numeric>  <character> <character> #> 1                       NA             0           NA      scan=1 #> 2                       NA             0           NA      scan=2 #> 3                       NA             0           NA      scan=3 #> 4                       NA             0           NA      scan=4 #> 5                       NA             0           NA      scan=5 #> ...                    ...           ...          ...         ... #> 194                     NA             0           NA    scan=194 #> 195                     NA             0           NA    scan=195 #> 196                     NA             0           NA    scan=196 #> 197                     NA             0           NA    scan=197 #> 198                     NA             0           NA    scan=198 #>     ionMobilityDriftTime scanWindowLowerLimit scanWindowUpperLimit spectrum_id_ #>                <numeric>            <numeric>            <numeric>    <integer> #> 1                     NA                   NA                   NA            1 #> 2                     NA                   NA                   NA            2 #> 3                     NA                   NA                   NA            3 #> 4                     NA                   NA                   NA            4 #> 5                     NA                   NA                   NA            5 #> ...                  ...                  ...                  ...          ... #> 194                   NA                   NA                   NA          194 #> 195                   NA                   NA                   NA          195 #> 196                   NA                   NA                   NA          196 #> 197                   NA                   NA                   NA          197 #> 198                   NA                   NA                   NA          198  ## Available variables spectraVariables(be) #>  [1] \"msLevel\"                  \"rtime\"                    #>  [3] \"acquisitionNum\"           \"scanIndex\"                #>  [5] \"mz\"                       \"intensity\"                #>  [7] \"dataStorage\"              \"dataOrigin\"               #>  [9] \"centroided\"               \"smoothed\"                 #> [11] \"polarity\"                 \"precScanNum\"              #> [13] \"precursorMz\"              \"precursorIntensity\"       #> [15] \"precursorCharge\"          \"collisionEnergy\"          #> [17] \"isolationWindowLowerMz\"   \"isolationWindowTargetMz\"  #> [19] \"isolationWindowUpperMz\"   \"peaksCount\"               #> [21] \"totIonCurrent\"            \"basePeakMZ\"               #> [23] \"basePeakIntensity\"        \"ionisationEnergy\"         #> [25] \"lowMZ\"                    \"highMZ\"                   #> [27] \"mergedScan\"               \"mergedResultScanNum\"      #> [29] \"mergedResultStartScanNum\" \"mergedResultEndScanNum\"   #> [31] \"injectionTime\"            \"filterString\"             #> [33] \"spectrumId\"               \"ionMobilityDriftTime\"     #> [35] \"scanWindowLowerLimit\"     \"scanWindowUpperLimit\"     #> [37] \"spectrum_id_\"              ## Access mz values mz(be) #> NumericList of length 198 #> [[1]] 104.553733825684 106.996170043945 ... 1002.67761230469 1004.47033691406 #> [[2]] 107.959617614746 109.964324951172 ... 991.343811035156 1002.79937744141 #> [[3]] 107.962753295898 112.021392822266 ... 964.238586425781 993.959167480469 #> [[4]] 105.970863342285 109.984230041504 ... 979.084838867188 986.755981445312 #> [[5]] 104.473876953125 106.999610900879 ... 1003.185546875 1003.46936035156 #> [[6]] 102.036674499512 107.963928222656 ... 993.781127929688 994.755920410156 #> [[7]] 104.272621154785 112.024925231934 ... 996.248046875 1001.64440917969 #> [[8]] 98.9297180175781 106.506416320801 ... 991.034484863281 997.045837402344 #> [[9]] 107.966445922852 109.385284423828 ... 995.031494140625 995.600463867188 #> [[10]] 108.965042114258 109.974197387695 ... 982.596313476562 989.777404785156 #> ... #> <188 more elements>  ## Subset the object to spectra in arbitrary order be_sub <- be[c(5, 1, 1, 2, 4, 100)] be_sub #> MsBackendSql with 6 spectra #>     msLevel precursorMz  polarity #>   <integer>   <numeric> <integer> #> 1         1          NA         1 #> 2         1          NA         1 #> 3         1          NA         1 #> 4         1          NA         1 #> 5         1          NA         1 #> 6         1          NA         1 #>  ... 34 more variables/columns. #>  Use  'spectraVariables' to list all of them. #> Database: /tmp/RtmpjVGmuK/file76664c5f5a0f  ## The internal spectrum IDs (primary keys from the database) be_sub$spectrum_id_ #> [1]   5   1   1   2   4 100  ## Add additional spectra variables be_sub$new_variable <- \"B\"  ## This variable is *cached* locally within the object (not inserted into ## the database) be_sub$new_variable #> [1] \"B\" \"B\" \"B\" \"B\" \"B\" \"B\""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-5","dir":"Changelog","previous_headings":"","what":"Changes in 1.5.1","title":"MsBackendSql 1.5","text":"Implement new extractByIndex() methods.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.5","title":"MsBackendSql 1.3","text":"Improve input argument check error message backendInitialize() MsBackendOfflineSql. Update documentation adding () function names.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3-1","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.4","title":"MsBackendSql 1.3","text":"Ensure primary keys database correct order backendInitialize().","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3-2","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.3","title":"MsBackendSql 1.3","text":"Import method generics ProtGenerics.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3-3","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.2","title":"MsBackendSql 1.3","text":"Add dedicated setBackend method MsBackendSql MsBackendOfflineSql backends (issue #17).","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-3-4","dir":"Changelog","previous_headings":"","what":"Changes in 1.3.1","title":"MsBackendSql 1.3","text":"Add description use/advantages different SQL database systems vignette.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.5","title":"MsBackendSql 1.1","text":"Add dbconn methods MsBackendSql MsBackendOfflineSql.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1-1","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.4","title":"MsBackendSql 1.1","text":"Improve performance createMsBackendSqlDatabase using also parallel processing peaksData call.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1-2","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.3","title":"MsBackendSql 1.1","text":"Add support setBackend MsBackendOfflineSql.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1-3","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.2","title":"MsBackendSql 1.1","text":"Mention documentation MsBackendSql can saved disk. Expand vignette adding related documentation.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-1-1-4","dir":"Changelog","previous_headings":"","what":"Changes in 1.1.1","title":"MsBackendSql 1.1","text":"Fix filterRt avoiding filter range infinite.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.7","title":"MsBackendSql 0.99","text":"Decrease required R version 4.2.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-1","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.6","title":"MsBackendSql 0.99","text":"Add mzR Suggests ensure package vignettes can build properly.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-2","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.5","title":"MsBackendSql 0.99","text":"Add MsBackendOfflineSql backend re-connects database query.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-3","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.4","title":"MsBackendSql 0.99","text":"Add backendBpparam method ensure parallel processing disabled MsBackendSql backend.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-4","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.3","title":"MsBackendSql 0.99","text":"Add backendMerge method. Add parameter data backendInitialize allow creating new MsBackendSql database store values data . enables use Spectra,setBackend convert backend MsBackendSql. Implement supportsSetBackend enable setBackend,Spectra,MsBackendSql.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-5","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.2","title":"MsBackendSql 0.99","text":"Evaluate validity MsBackendSql using full unit test suite Spectra package.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-6","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.1","title":"MsBackendSql 0.99","text":"Address Kayla’s package review comments.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-99-7","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.0","title":"MsBackendSql 0.99","text":"Prepare package submission Bioconductor.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-98","dir":"Changelog","previous_headings":"","what":"Changes in 0.98.1","title":"MsBackendSql 0.98","text":"Rename MsqlBackend MsBackendSql.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-98-1","dir":"Changelog","previous_headings":"","what":"Changes in 0.98.0","title":"MsBackendSql 0.98","text":"Add vignette.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-1","dir":"Changelog","previous_headings":"","what":"Changes in 0.1.0","title":"MsBackendSql 0.1","text":"Add parameter blob allow storing m/z intensity values BLOB data type database. MsBackendSql use different functions retrieve data database type storage.","code":""},{"path":[]},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-0","dir":"Changelog","previous_headings":"","what":"Changes in 0.0.5","title":"MsBackendSql 0.0","text":"Add filterMsLevel method. Add filterRt method. Add filterDataOrigin method. Add filterPrecursorMzRange method. Add filterPrecursorMzValues method.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-0-1","dir":"Changelog","previous_headings":"","what":"Changes in 0.0.4","title":"MsBackendSql 0.0","text":"Add optional parameter tempfile.","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-0-2","dir":"Changelog","previous_headings":"","what":"Changes in 0.0.3","title":"MsBackendSql 0.0","text":"Add peaksVariables methods add support parameter columns peaksData (Requires Spectra version 1.15.17).","code":""},{"path":"https://rformassspectrometry.github.io/MsBackendSql/news/index.html","id":"changes-in-0-0-3","dir":"Changelog","previous_headings":"","what":"Changes in 0.0.2","title":"MsBackendSql 0.0","text":"First full implementation MsBackendSql.","code":""}]