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<h1>Calculate the correlation relationshipt among all covariates
in the metadata table</h1>
<div class="hidden name"><code>degCorCov.Rd</code></div>
</div>
<div class="ref-description">
<p>This function will calculate the correlation among
all columns in the metadata</p>
</div>
<pre class="usage"><span class='fu'>degCorCov</span>(<span class='no'>metadata</span>, <span class='kw'>fdr</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</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>metadata</th>
<td><p>data.frame with samples metadata.</p></td>
</tr>
<tr>
<th>fdr</th>
<td><p>numeric value to use as cutoff to determine
the minimum fdr to consider significant correlations
between pcs and covariates.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Parameters to pass to <code><a href='https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html'>ComplexHeatmap::Heatmap()</a></code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>: list:
a) cor, data.frame with pair-wise correlations, pvalues, FDR
b) corMat, data.frame with correlation matrix
c) fdrMat, data.frame with FDR matrix
b) plot, Heatmap plot of correlation matrix</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'>dse</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'>cor</span> <span class='kw'><-</span> <span class='fu'>degCorCov</span>(<span class='fu'>colData</span>(<span class='no'>dse</span>))</div><div class='output co'>#> <span class='warning'>Warning: The input is a data frame, convert it to the matrix.</span></div><div class='img'><img src='degCorCov-1.png' alt='' width='700' height='433' /></div></pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
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<h2>Author</h2>
<p>: Lorena Pantano, Kenneth Daily and Thanneer Malai Perumal</p>
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