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<h1>Filter genes by group</h1>
<div class="hidden name"><code>degFilter.Rd</code></div>
</div>
<div class="ref-description">
<p>This function will keep only rows that have a minimum counts of
1 at least in a <code>min</code> number of samples (default 80<!-- %). --></p>
</div>
<pre class="usage"><span class='fu'>degFilter</span>(<span class='no'>counts</span>, <span class='no'>metadata</span>, <span class='no'>group</span>, <span class='kw'>min</span> <span class='kw'>=</span> <span class='fl'>0.8</span>, <span class='kw'>minreads</span> <span class='kw'>=</span> <span class='fl'>0</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>counts</th>
<td><p>Matrix with expression data, columns are samples
and rows are genes or other feature.</p></td>
</tr>
<tr>
<th>metadata</th>
<td><p>Data.frame with information about
each column in counts matrix. Rownames should match
<code><a href='https://rdrr.io/r/base/colnames.html'>colnames(counts)</a></code>.</p></td>
</tr>
<tr>
<th>group</th>
<td><p>Character column in metadata used to
group samples and applied the cutoff.</p></td>
</tr>
<tr>
<th>min</th>
<td><p>Percentage value indicating the minimum
number of samples in each group that should have
more than 0 in count matrix.</p></td>
</tr>
<tr>
<th>minreads</th>
<td><p>Integer minimum number of reads to consider
a feature expressed.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>count <code>matrix</code> after filtering genes (features)
with not enough expression in any group.</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'>SummarizedExperiment</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'>c</span> <span class='kw'><-</span> <span class='fu'>degFilter</span>(<span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>assays</a></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'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>colData</a></span>(<span class='no'>humanGender</span>)[<span class='no'>idx</span>,], <span class='st'>"group"</span>, <span class='kw'>min</span><span class='kw'>=</span><span class='fl'>1</span>)</div></pre>
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