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ld_clump_api.html
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ld_clump_api.html
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<h1>Perform clumping on the chosen variants using through API</h1>
<small class="dont-index">Source: <a href='https://github.com/mrcieu/ieugwasr/blob/master/R/ld_clump.R'><code>R/ld_clump.R</code></a></small>
<div class="hidden name"><code>ld_clump_api.Rd</code></div>
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<div class="ref-description">
<p>Perform clumping on the chosen variants using through API</p>
</div>
<pre class="usage"><span class='fu'>ld_clump_api</span>(
<span class='no'>dat</span>,
<span class='kw'>clump_kb</span> <span class='kw'>=</span> <span class='fl'>10000</span>,
<span class='kw'>clump_r2</span> <span class='kw'>=</span> <span class='fl'>0.1</span>,
<span class='no'>clump_p</span>,
<span class='kw'>pop</span> <span class='kw'>=</span> <span class='st'>"EUR"</span>,
<span class='kw'>access_token</span> <span class='kw'>=</span> <span class='fu'><a href='check_access_token.html'>check_access_token</a></span>()
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>dat</th>
<td><p>Dataframe. Must have a variant name column ("variant") and pval column called "pval". If id is present then clumping will be done per unique id.</p></td>
</tr>
<tr>
<th>clump_kb</th>
<td><p>Clumping kb window. Default is very strict, 10000</p></td>
</tr>
<tr>
<th>clump_r2</th>
<td><p>Clumping r2 threshold. Default is very strict, 0.001</p></td>
</tr>
<tr>
<th>clump_p</th>
<td><p>Clumping sig level for index variants. Default = 1 (i.e. no threshold)</p></td>
</tr>
<tr>
<th>pop</th>
<td><p>Super-population to use as reference panel. Default = "EUR". Options are EUR, SAS, EAS, AFR, AMR</p></td>
</tr>
<tr>
<th>access_token</th>
<td><p>Google OAuth2 access token. Used to authenticate level of access to data#' @return Data frame of only independent variants</p></td>
</tr>
</table>
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