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<!DOCTYPE html>
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<title>GWAS summary data sources connected to analytical tools • gwasglue</title>
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<script src="pkgdown.js"></script><meta property="og:title" content="GWAS summary data sources connected to analytical tools">
<meta property="og:description" content="Many tools exist that use GWAS summary data for colocalisation, fine mapping, Mendelian randomization, visualisation, etc. This package is a conduit that connects R packages that can retrieve GWAS summary data to various tools for analysing those data.">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.0.9000</span>
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<a href="articles/cojo.html">Conditional analysis of VCF files</a>
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<a href="articles/colocalisation.html">Genetic colocalisation</a>
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<a href="articles/finemapping.html">Clumping and finemapping</a>
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<a href="articles/gwas2020.html">Major changes to the IEU GWAS resources for 2020</a>
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<div id="gwasglue" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
<a href="#gwasglue" class="anchor"></a>gwasglue</h1></div>
<!-- badges: start -->
<p><strong>Under development</strong></p>
<p>This R package serves as a conduit between packages that can read or query GWAS summary data, and packages that can analyse GWAS summary data. Here is where it lies in the general ecosystem of GWAS data and analysis:</p>
<p><img src="https://drive.google.com/uc?id=15w33jAaI6lAKINfLlNw343njUuPd4M6i" alt="schematic"></p>
<p>The figure above depicts a set of packages that we plan to connect to. Here is a list of what has been done and what is still to do:</p>
<div id="data-sources" class="section level4">
<h4 class="hasAnchor">
<a href="#data-sources" class="anchor"></a>Data sources</h4>
<ul>
<li><a href="https://github.com/mrcieu/ieugwasr">ieugwasr</a></li>
<li><a href="https://github.com/mrcieu/gwasvcf">gwasvcf</a></li>
</ul>
</div>
<div id="finemapping" class="section level4">
<h4 class="hasAnchor">
<a href="#finemapping" class="anchor"></a>Finemapping</h4>
<ul>
<li><a href="https://github.com/variani/finemapr">finemapr</a></li>
<li><a href="http://www.christianbenner.com/">FINEMAP</a></li>
<li><a href="https://github.com/gkichaev/PAINTOR_V3.0">PAINTOR</a></li>
<li><a href="https://github.com/fhormoz/caviar">CAVIAR</a></li>
<li>
<a href="https://stephenslab.github.io/susie-paper/index.html">SuSIE</a> - TODO</li>
<li>
<a href="https://github.com/pjnewcombe/R2BGLiMS">JAM</a> - TODO</li>
</ul>
</div>
<div id="colocalisation" class="section level4">
<h4 class="hasAnchor">
<a href="#colocalisation" class="anchor"></a>Colocalisation</h4>
<ul>
<li><a href="https://cloud.r-project.org/web/packages/coloc/index.html">coloc</a></li>
<li>
<a href="http://cnsgenomics.com/software/gsmr/">HEIDI</a> - TODO</li>
<li>
<a href="https://github.com/fhormoz/caviar">eCAVIAR</a> - TODO</li>
<li>
<a href="https://github.com/hakyimlab/MetaXcan">S-Predixcan</a> - TODO</li>
</ul>
</div>
<div id="mendelian-randomization" class="section level4">
<h4 class="hasAnchor">
<a href="#mendelian-randomization" class="anchor"></a>Mendelian randomization</h4>
<ul>
<li><a href="https://github.com/mrcieu/TwoSampleMR">TwoSampleMR</a></li>
<li>
<a href="https://cran.r-project.org/web/packages/MendelianRandomization/index.html">MendelianRandomization</a> - port from TwoSampleMR</li>
<li>
<a href="https://github.com/WSpiller/RadialMR">RadialMR</a> - port from TwoSampleMR</li>
<li>
<a href="https://github.com/rondolab/MR-PRESSO">MRPRESSO</a> - port from TwoSampleMR</li>
<li>
<a href="http://cnsgenomics.com/software/gsmr/">GSMR</a> - TODO</li>
<li>
<a href="https://github.com/gqi/MRMix">MRMix</a> - TODO</li>
</ul>
</div>
<div id="visualisation" class="section level4">
<h4 class="hasAnchor">
<a href="#visualisation" class="anchor"></a>Visualisation</h4>
<ul>
<li><a href="https://github.com/jrs95/gassocplot">gassocplot</a></li>
<li>Locus zoom plots e.g. [<a href="https://github.com/jrs95/gassocplot" class="uri">https://github.com/jrs95/gassocplot</a>] - TODO</li>
</ul>
</div>
<div id="installation" class="section level2">
<h2 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h2>
<p>You can install the development version of gwasglue with:</p>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span><span class="op">(</span><span class="st">"mrcieu/gwasglue"</span><span class="op">)</span></pre></div>
</div>
<div id="usage" class="section level2">
<h2 class="hasAnchor">
<a href="#usage" class="anchor"></a>Usage</h2>
<p>See vignettes etc here: <a href="https://mrcieu.github.io/gwasglue">https://mrcieu.github.io/gwasglue</a>.</p>
</div>
<div id="reference-datasets" class="section level2">
<h2 class="hasAnchor">
<a href="#reference-datasets" class="anchor"></a>Reference datasets</h2>
<p>Example GWAS VCF (GIANT 2010 BMI):</p>
<ul>
<li><a href="http://fileserve.mrcieu.ac.uk/vcf/IEU-a-2.vcf.gz" class="uri">http://fileserve.mrcieu.ac.uk/vcf/IEU-a-2.vcf.gz</a></li>
<li><a href="http://fileserve.mrcieu.ac.uk/vcf/IEU-a-2.vcf.gz.tbi" class="uri">http://fileserve.mrcieu.ac.uk/vcf/IEU-a-2.vcf.gz.tbi</a></li>
</ul>
<p>Updated 1000 genomes LD reference panels (multiple populations):</p>
<ul>
<li><a href="http://fileserve.mrcieu.ac.uk/ld/1kg.v3.tgz" class="uri">http://fileserve.mrcieu.ac.uk/ld/1kg.v3.tgz</a></li>
</ul>
<p>1kg European reference panel for LD (legacy):</p>
<ul>
<li><a href="http://fileserve.mrcieu.ac.uk/ld/data_maf0.01_rs_ref.tgz" class="uri">http://fileserve.mrcieu.ac.uk/ld/data_maf0.01_rs_ref.tgz</a></li>
</ul>
<p>1kg vcf harmonised against human genome reference:</p>
<ul>
<li><a href="http://fileserve.mrcieu.ac.uk/vcf/1kg_v3_nomult.vcf.gz" class="uri">http://fileserve.mrcieu.ac.uk/vcf/1kg_v3_nomult.vcf.gz</a></li>
<li><a href="http://fileserve.mrcieu.ac.uk/vcf/1kg_v3_nomult.vcf.gz.tbi" class="uri">http://fileserve.mrcieu.ac.uk/vcf/1kg_v3_nomult.vcf.gz.tbi</a></li>
</ul>
</div>
<div id="contributing-to-the-resource" class="section level2">
<h2 class="hasAnchor">
<a href="#contributing-to-the-resource" class="anchor"></a>Contributing to the resource</h2>
<p>For any <code><analysis></code> package we create a new file called <code>R/<analysis>.r</code> which contains two functions:</p>
<ul>
<li><code>gwasvcf_to_<analysis></code></li>
<li><code>ieugwasr_to_<analysis></code></li>
</ul>
<p>For an example, see the <code>R/TwoSampleMR.r</code> file, which contains the functions <code>gwasvcf_to_TwoSampleMR</code> and <code>ieugwasr_to_TwoSampleMR</code>.</p>
</div>
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<h2>Links</h2>
<ul class="list-unstyled">
<li>Browse source code at <br><a href="https://github.com/mrcieu/gwasglue/">https://github.com/mrcieu/gwasglue/</a>
</li>
<li>Report a bug at <br><a href="https://github.com/mrcieu/gwasglue/issues">https://github.com/mrcieu/gwasglue/issues</a>
</li>
</ul>
</div>
<div class="license">
<h2>License</h2>
<ul class="list-unstyled">
<li><a href="LICENSE.html">Full license</a></li>
<li><small><a href="https://opensource.org/licenses/mit-license.php">MIT</a> + file <a href="LICENSE-text.html">LICENSE</a></small></li>
</ul>
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<div class="developers">
<h2>Developers</h2>
<ul class="list-unstyled">
<li>Gibran Hemani <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-0920-1055" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
</ul>
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<h2>Dev status</h2>
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<li><a href="https://www.tidyverse.org/lifecycle/#experimental"><img src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" alt="Lifecycle: experimental"></a></li>
<li><a href="https://travis-ci.org/MRCIEU/gwasglue"><img src="https://travis-ci.org/MRCIEU/gwasglue.svg?branch=master" alt="Travis build status"></a></li>
<li><a href="https://codecov.io/gh/MRCIEU/gwasglue?branch=master"><img src="https://codecov.io/gh/MRCIEU/gwasglue/branch/master/graph/badge.svg" alt="Codecov test coverage"></a></li>
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<p>Developed by Gibran Hemani.</p>
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