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<!DOCTYPE html>
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<title>Multivariate Adaptive Shrinkage • mashr</title>
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<div id="mashr-multivariate-adaptive-shrinkage-in-r" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
<a href="#mashr-multivariate-adaptive-shrinkage-in-r" class="anchor"></a>mashr: Multivariate Adaptive Shrinkage in R</h1></div>
<p><em>Welcome to mashr!</em> This package implements methods to estimate and test many effects in many conditions (or many effects on many outcomes).</p>
<p>The methods use Empirical Bayes methods to estimate patterns of similarity among conditions, and then exploit those patterns of similarity among conditions to improve accuracy of effect estimates. See <a href="http://biorxiv.org/content/early/2017/05/09/096552">Urbut et al</a> for details of the model and methods.</p>
<p>Note that this R package is a refactoring of the code originally used to create results for the paper. The original package code is <a href="http://github.com/stephenslab/mashr-paper">here</a>.</p>
<div id="quick-start" class="section level2">
<h2 class="hasAnchor">
<a href="#quick-start" class="anchor"></a>Quick Start</h2>
<ol>
<li><p>Follow the setup instructions below.</p></li>
<li><p>See the <a href="https://stephenslab.github.io/mashr/articles/intro_mash.html">Introductory Vignette</a> for an introduction to mashr.</p></li>
<li><p>Then work through the other vignettes to learn more about mashr: <a href="https://stephenslab.github.io/mashr/articles/intro_mash_dd.html">Introduction to mash: data-driven covariances</a> and <a href="https://stephenslab.github.io/mashr/articles/simulate_noncanon.html">Simulation with non-canonical matrices</a>.</p></li>
</ol>
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<div id="setup" class="section level2">
<h2 class="hasAnchor">
<a href="#setup" class="anchor"></a>Setup</h2>
<p>Please follow these steps to install the <a href="https://github.com/stephenslab/mashr/releases/tag/v0.2-6">latest version of the mashr package</a>:</p>
<ol>
<li>In R, install these three R packages from CRAN:</li>
</ol>
<p><code>R install.packages(c("assertthat","mvtnorm","rmeta"))</code></p>
<ol>
<li>Optionally, install the package used for memory profiling:</li>
</ol>
<p><code>R install.packages("profmem")</code></p>
<ol>
<li><p>Optionally, install MOSEK and the Rmosek package, for faster optimization in the <code>ashr</code> package. See the <a href="https://github.com/stephens999/ashr">ashr Github repository</a> for details.</p></li>
<li><p>Install the <a href="https://github.com/jobovy/extreme-deconvolution#installation">ExtremeDeconvolution R package</a>. Note that you will need to link to the <a href="https://www.gnu.org/software/gsl">GNU Scientific Library</a> to build this package.</p></li>
<li><p>Once you have installed all these packages, you can install and load the <a href="https://github.com/stephenslab/mashr/releases/tag/v0.2-6">latest release</a> of the <code>mashr</code> package:</p></li>
</ol>
<p><code>R library(devtools) install_github("stephenslab/mashr@v0.2-6") library(mashr)</code></p>
<p>This command should automatically retrieve and install the <code>ashr</code> package from Github. If it does not, install ashr separately using devtools:</p>
<p><code>R library(devtools) install_github("stephens999/ashr")</code></p>
<p>Alternatively, if you have cloned the repository locally, you can install the package by following these steps:</p>
<p><code>R CMD build mashr R CMD INSTALL mashr_0.2-6.tar.gz</code></p>
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<div id="developer-notes" class="section level2">
<h2 class="hasAnchor">
<a href="#developer-notes" class="anchor"></a>Developer notes</h2>
<ul>
<li><p>When any changes are made to <code>roxygen2</code> markup or the C++ code in the src directory, simply run <code><a href="http://www.rdocumentation.org/packages/devtools/topics/document">devtools::document()</a></code> to update the <a href="src/RcppExports.cpp">RcppExports.cpp</a>, the package namespaces (see <a href="NAMESPACE" class="uri">NAMESPACE</a>), and the package documentation files (in the man directory),</p></li>
<li><p>These are the R commands to build the website (make sure you are connected to Internet while running these commands):</p></li>
</ul>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(pkgdown)
<span class="kw"><a href="https://pkgdown.r-lib.org/reference/build_site.html">build_site</a></span>(<span class="dt">mathjax =</span> <span class="ot">FALSE</span>)</code></pre></div>
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<div id="citation" class="section level2">
<h2 class="hasAnchor">
<a href="#citation" class="anchor"></a>Citation</h2>
<p>If the data or code in this repository are useful for your research project, please cite our preprint:</p>
<p>S M Urbut, G Wang, M Stephens. Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. <em>bioRxiv</em> <a href="doi:10.1101/096552" class="uri">doi:10.1101/096552</a>.</p>
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<h2>Links</h2>
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<li>Browse source code at <br><a href="http://github.com/stephenslab/mashr">http://github.com/stephenslab/mashr</a>
</li>
<li>Report a bug at <br><a href="http://github.com/stephenslab/mashr/issues">http://github.com/stephenslab/mashr/issues</a>
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</ul>
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<h2>License</h2>
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<a href="https://opensource.org/licenses/BSD-3-Clause">BSD_3_clause</a> + file <a href="LICENSE-text.html">LICENSE</a>
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<div class="developers">
<h2>Developers</h2>
<ul class="list-unstyled">
<li>Matthew Stephens <br><small class="roles"> Author, maintainer </small> </li>
<li>Sarah Urbut <br><small class="roles"> Author </small> </li>
<li>Gao Wang <br><small class="roles"> Author </small> </li>
<li>Yuxin Zou <br><small class="roles"> Author </small> </li>
<li>Peter Carbonetto <br><small class="roles"> Author </small> </li>
</ul>
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<h2>Dev status</h2>
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<p>Developed by Matthew Stephens, Sarah Urbut, Gao Wang, Yuxin Zou, Peter Carbonetto.</p>
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