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<h1>Distribution of the standard desviation of
DE genes compared to the background</h1>
<div class="hidden name"><code>degVB.Rd</code></div>
</div>
<div class="ref-description">
<p>Distribution of the standard desviation of
DE genes compared to the background</p>
</div>
<pre class="usage"><span class='fu'>degVB</span>(<span class='no'>tags</span>, <span class='no'>group</span>, <span class='no'>counts</span>, <span class='kw'>pop</span> <span class='kw'>=</span> <span class='fl'>400</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>tags</th>
<td><p>List of genes that are DE.</p></td>
</tr>
<tr>
<th>group</th>
<td><p>Character vector with group name for each sample in the
same order than counts column names.</p></td>
</tr>
<tr>
<th>counts</th>
<td><p>matrix with counts for each samples and each gene.
Should be same length than pvalues vector.</p></td>
</tr>
<tr>
<th>pop</th>
<td><p>Number of random samples taken for background comparison.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>ggplot2 object</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>humanGender</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>DESeq2</span>)
<span class='no'>idx</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>:<span class='fl'>10</span>, <span class='fl'>75</span>:<span class='fl'>85</span>)
<span class='no'>dds</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/DESeqDataSet.html'>DESeqDataSetFromMatrix</a></span>(<span class='fu'>assays</span>(<span class='no'>humanGender</span>)<span class='kw'>[[</span><span class='fl'>1</span>]][<span class='fl'>1</span>:<span class='fl'>1000</span>, <span class='no'>idx</span>],
<span class='fu'>colData</span>(<span class='no'>humanGender</span>)[<span class='no'>idx</span>,], <span class='kw'>design</span><span class='kw'>=</span>~<span class='no'>group</span>)
<span class='no'>dds</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/DESeq.html'>DESeq</a></span>(<span class='no'>dds</span>)</div><div class='output co'>#> <span class='message'>using pre-existing size factors</span></div><div class='output co'>#> <span class='message'>estimating dispersions</span></div><div class='output co'>#> <span class='message'>gene-wise dispersion estimates</span></div><div class='output co'>#> <span class='message'>mean-dispersion relationship</span></div><div class='output co'>#> <span class='message'>final dispersion estimates</span></div><div class='output co'>#> <span class='message'>fitting model and testing</span></div><div class='output co'>#> <span class='message'>-- replacing outliers and refitting for 1 genes</span>
#> <span class='message'>-- DESeq argument 'minReplicatesForReplace' = 7 </span>
#> <span class='message'>-- original counts are preserved in counts(dds)</span></div><div class='output co'>#> <span class='message'>estimating dispersions</span></div><div class='output co'>#> <span class='message'>fitting model and testing</span></div><div class='input'><span class='no'>res</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/results.html'>results</a></span>(<span class='no'>dds</span>)
<span class='fu'>degVB</span>(<span class='fu'><a href='https://rdrr.io/r/base/row.names.html'>row.names</a></span>(<span class='no'>res</span>)[<span class='fl'>1</span>:<span class='fl'>20</span>], <span class='fu'>colData</span>(<span class='no'>dds</span>)<span class='kw'>[[</span><span class='st'>"group"</span>]],
<span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/counts.html'>counts</a></span>(<span class='no'>dds</span>, <span class='kw'>normalized</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='img'><img src='degVB-1.png' alt='' width='700' height='433' /></div></pre>
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<h2>Contents</h2>
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<li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
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