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<h1 class="title toc-ignore">MASH analysis of GTEx data from Urbut et al (2017)</h1>
<h4 class="author"><em>Peter Carbonetto</em></h4>
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<p><strong>Last updated:</strong> 2018-05-07</p>
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<p></details></p>
<hr />
<p>In this directory, we provide all the instructions for reproducing the GTEx results from: “Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions” (Urbut et al 2017).</p>
<p>Figure 3:<a href="Fig.Uk3.html">Summary of primary patterns identified by mash in GTEx data</a></p>
<p>Figure 4:<a href="Fig.GTExExamples.html">Examples illustrating of how mash uses patterns of sharing to inform effect estimates in the GTEx data.</a></p>
<p>Figure 5:<a href="Fig.SharingHist.pdf">Histogram of Sharing</a></p>
<p>Figure 6:<a href="Fig.SharingMag.html">Pairwise sharing by magnitude of eQTL among tissues</a></p>
<p>Supplementary Figure 1:<a href="Fig.SampleSize.html">Sample sizes and effective sample sizes from mash analysis across tissues</a></p>
<p>Supplementary Figure 2:There are 4 figures here:</p>
<p><a href="Fig.Uk2.pdf">Summary of covariance matrices Uk with largest estimated weight (> 1%) in GTEx data:Uk2</a></p>
<p><a href="Fig.Uk4.html">Summary of covariance matrices Uk with largest estimated weight (> 1%) in GTEx data:Uk4</a></p>
<p><a href="Fig.Uk5.html">Summary of covariance matrices Uk with largest estimated weight (> 1%) in GTEx data:Uk5</a></p>
<p><a href="Fig.Uk8.html">Summary of covariance matrices Uk with largest estimated weight (> 1%) in GTEx data:Uk8</a></p>
<p>Supplementary Figure 3: Illustration of how Linkage Disequilibrium can impact effect estimate <a href="TwoSNP.html">table</a> and <a href="TwoSNPPlot.pdf">figure</a></p>
<p>Supplementary Figure 4:<a href="Fig.SharingSign.html">Pairwise Sharing By Sign</a></p>
<p>Supplementary Figure 5:<a href="Fig.Tspecific.html">Number of “tissue-specific eQTLs” in each tissues.</a></p>
<p>Supplementary Figure 6:<a href="Fig.ExpressionAnalysis.html">Expression levels in genes with “tissue-specific eQTLs” are similar to those in other genes</a></p>
<p>Table 1: Heterogeneity Analysis <a href="Table.hettablesim.html">Simulation</a> and <a href="Table.HeterogeneityTables.html">Data</a>.</p>
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