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<!DOCTYPE html>
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<title>R interface to the IEU GWAS database API • ieugwasr</title>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
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<a href="articles/guide.html">Perform fast queries against a massive database of complete GWAS summary data</a>
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<a href="articles/timings.html">Comparison of rsid vs chr:pos lookup in ElasticSearch</a>
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<div id="perform-fast-queries-in-r-against-a-massive-database-of-complete-gwas-summary-data" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
<a href="#perform-fast-queries-in-r-against-a-massive-database-of-complete-gwas-summary-data" class="anchor"></a>Perform fast queries in R against a massive database of complete GWAS summary data</h1></div>
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<p>The <a href="https://gwas.mrcieu.ac.uk/">IEU GWAS database</a> comprises over 10,000 curated, QC’d and harmonised complete GWAS summary datasets and can be queried using an API. See <a href="https://gwas-api.mrcieu.ac.uk/docs">here</a> for documentation on the API itself. This R package is a wrapper to make generic calls to the API, plus convenience functions for specific queries.</p>
<p>Methods currently implemented:</p>
<ul>
<li>Get meta data about specific or all studies</li>
<li>Obtain the top hits (with on the fly clumping as an option) from each of the GWAS datasets. Clumping and significance thresholds can be specified</li>
<li>Obtain the summary results of specific variants across specific studies. LD-proxy lookups are performed automatically if a specific variant is absent from a study</li>
<li>Query a genomic region in a GWAS dataset, e.g. for fine mapping or colocalisation analysis</li>
<li>Perform PheWAS</li>
</ul>
<p>There are a few convenience functions also:</p>
<ul>
<li>Query dbSNP data, allowing conversion between chromosome:position and rsids and getting annotations</li>
<li>Perform LD clumping using the server, or locally</li>
<li>Obtain LD matrices for a list of SNPs using the server or locally (e.g. for fine mapping, colocalisation or Mendelian randomization)</li>
</ul>
<p>See [<a href="https://github.com/MRCIEU/gwasglue" class="uri">https://github.com/MRCIEU/gwasglue</a>] for information about how to connect the genotype and LD data to other packages involving colocalisation, finemapping, visualisation and MR.</p>
<div id="installation" class="section level2">
<h2 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h2>
<p>You can install the developer version of ieugwasr with:</p>
<div class="sourceCode" id="cb1"><pre class="r"><span class="kw pkg">devtools</span><span class="kw ns">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span>(<span class="st">"mrcieu/ieugwasr"</span>)</pre></div>
<p>Browse the vignettes etc for information on how to use this package: <a href="https://mrcieu.github.io/ieugwasr/">https://mrcieu.github.io/ieugwasr/</a></p>
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<h2>Links</h2>
<ul class="list-unstyled">
<li>Browse source code at <br><a href="https://github.com/mrcieu/ieugwasr/">https://github.com/mrcieu/ieugwasr/</a>
</li>
<li>Report a bug at <br><a href="https://github.com/mrcieu/ieugwasr/issues">https://github.com/mrcieu/ieugwasr/issues</a>
</li>
</ul>
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<div class="license">
<h2>License</h2>
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<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>
</div>
<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>
</div>
<div class="dev-status">
<h2>Dev status</h2>
<ul class="list-unstyled">
<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/ieugwasr"><img src="https://travis-ci.org/MRCIEU/ieugwasr.svg?branch=master" alt="Travis-CI build status"></a></li>
<li><a href="https://codecov.io/github/mrcieu/ieugwasr"><img src="https://codecov.io/github/mrcieu/ieugwasr/branch/master/graphs/badge.svg" alt="codecov"></a></li>
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<p>Developed by Gibran Hemani.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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