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<h1>Remove transversions (C->T and G->A substitutions)</h1>
<small class="dont-index">Source: <a href='https://github.com/bodkan/admixr/blob/master/R/eigenstrat.R'><code>R/eigenstrat.R</code></a></small>
<div class="hidden name"><code>transversions_only.Rd</code></div>
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<div class="ref-description">
<p>Remove substitutions that are more likely to be a result of ancient DNA
damage (C->T and G->A substitutions).</p>
</div>
<pre class="usage"><span class='fu'>transversions_only</span>(<span class='no'>data</span>, <span class='kw'>outfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/tempfile.html'>tempfile</a></span>(<span class='kw'>fileext</span> <span class='kw'>=</span> <span class='st'>".snp"</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>outfile</th>
<td><p>Path to an output snp file with coordinates of excluded sites.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Updated S3 EIGENSTRAT data object with an additional 'exclude' slot
specifying the path to the set of SNPs to be removed from a downstream
analysis.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># download an example genomic 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='kw'>dirname</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/tempfile.html'>tempdir</a></span>()))
<span class='co'># perform the calculation only on transversions</span>
<span class='no'>snps_tv</span> <span class='kw'><-</span> <span class='fu'>transversions_only</span>(<span class='no'>snps</span>)
<span class='no'>results_d</span> <span class='kw'><-</span> <span class='fu'><a href='f4ratio.html'>d</a></span>(<span class='kw'>W</span> <span class='kw'>=</span> <span class='st'>"French"</span>, <span class='kw'>X</span> <span class='kw'>=</span> <span class='st'>"Dinka"</span>, <span class='kw'>Y</span> <span class='kw'>=</span> <span class='st'>"Altai"</span>, <span class='kw'>Z</span> <span class='kw'>=</span> <span class='st'>"Chimp"</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>snps_tv</span>)</div></pre>
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