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<h1>Calculate ancestry proportions in a set of target populations.</h1>
<small class="dont-index">Source: <a href='https://github.com/bodkan/admixr/blob/master/R/wrappers.R'><code>R/wrappers.R</code></a></small>
<div class="hidden name"><code>qpAdm.Rd</code></div>
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<div class="ref-description">
<p>Calculate ancestry proportions in a set of target populations.</p>
</div>
<pre class="usage"><span class='fu'>qpAdm</span>(
<span class='no'>data</span>,
<span class='no'>target</span>,
<span class='no'>sources</span>,
<span class='no'>outgroups</span>,
<span class='kw'>outdir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>allsnps</span> <span class='kw'>=</span> <span class='st'>"YES"</span>, <span class='kw'>summary</span> <span class='kw'>=</span> <span class='st'>"YES"</span>, <span class='kw'>details</span> <span class='kw'>=</span> <span class='st'>"YES"</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>data</th>
<td><p>EIGENSTRAT data object.</p></td>
</tr>
<tr>
<th>target</th>
<td><p>Vector of target populations (evaluated one at a time).</p></td>
</tr>
<tr>
<th>sources</th>
<td><p>Source populations related to true ancestors.</p></td>
</tr>
<tr>
<th>outgroups</th>
<td><p>Outgroup populations.</p></td>
</tr>
<tr>
<th>outdir</th>
<td><p>Where to put all generated files (temporary directory by default).</p></td>
</tr>
<tr>
<th>params</th>
<td><p>Named list of parameters and their values.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>List of three components:
1. estimated ancestry proportions
2. ranks statistics
3. analysis of patterns (all possible subsets of ancestry sources).</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># download example data set and prepare it for analysis</span>
<span class='no'>snps</span> <span class='kw'><-</span> <span class='fu'><a href='eigenstrat.html'>eigenstrat</a></span>(<span class='fu'><a href='download_data.html'>download_data</a></span>())
<span class='co'># estimate the proportion of Neandertal ancestry in a French</span>
<span class='co'># individual and other associated qpAdm statistics (see detailed</span>
<span class='co'># description in the tutorial vignette)</span>
<span class='no'>result</span> <span class='kw'><-</span> <span class='fu'>qpAdm</span>(
<span class='kw'>target</span> <span class='kw'>=</span> <span class='st'>"French"</span>,
<span class='kw'>sources</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Vindija"</span>, <span class='st'>"Yoruba"</span>),
<span class='kw'>outgroups</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Chimp"</span>, <span class='st'>"Denisova"</span>, <span class='st'>"Altai"</span>),
<span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>snps</span>
)</div></pre>
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