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<title>Distribution of gene ratios used to calculate Size Factors. — degCheckFactors • DEGreport</title>
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<h1>Distribution of gene ratios used to calculate Size Factors.</h1>
<div class="hidden name"><code>degCheckFactors.Rd</code></div>
</div>
<div class="ref-description">
<p>This function check the median ratio normalization used by
DESeq2 and similarly by edgeR to visualy check whether
the median is the best size factor to represent depth.</p>
</div>
<pre class="usage"><span class='fu'>degCheckFactors</span>(<span class='no'>counts</span>, <span class='kw'>each</span> <span class='kw'>=</span> <span class='fl'>FALSE</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 counts for each samples and each gene.
row number should be the same length than pvalues vector.</p></td>
</tr>
<tr>
<th>each</th>
<td><p>Plot each sample separately.</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="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function will plot the gene ratios for each sample. To calculate
the ratios, it follows the simliar logic than DESeq2/edgeR uses, where the expression
of each gene is divided by the mean expression of that gene. The distribution
of the ratios should approximate to a normal shape and the factors should be similar
to the median of distributions. If some samples show different distribution,
the factor may be bias due to some biological or technical factor.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<ul>
<li><p>Code to calculate size factors comes from
<code><a href='https://rdrr.io/pkg/DESeq2/man/estimateSizeFactorsForMatrix.html'>DESeq2::estimateSizeFactorsForMatrix()</a></code>.</p></li>
</ul>
<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='fu'>degCheckFactors</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'>10</span>])</div><div class='output co'>#> <span class='warning'>Warning: Removed 3 rows containing non-finite values (stat_density).</span></div><div class='img'><img src='degCheckFactors-1.png' alt='' width='700' height='433' /></div></pre>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
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<li><a href="#examples">Examples</a></li>
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