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<h1>Reference</h1>
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<col class="alias" />
<col class="title" />
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<h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
<p class="section-desc"></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="DEGSet.html">DEGSet()</a></code> <code><a href="DEGSet.html">DEGSet()</a></code> <code><a href="DEGSet.html">as.DEGSet()</a></code> </p>
</td>
<td><p>DEGSet</p></td>
</tr><tr>
<td>
<p><code><a href="DEGreport-deprecated.html">DEGreport-package</a></code> </p>
</td>
<td><p>Deprecated functions in package DEGreport</p></td>
</tr><tr>
<td>
<p><code><a href="createReport.html">createReport()</a></code> </p>
</td>
<td><p>Create report of RNAseq DEG anlaysis</p></td>
</tr><tr>
<td>
<p><code><a href="deg.html">deg()</a></code> </p>
</td>
<td><p>Method to get all table stored for an specific comparison</p></td>
</tr><tr>
<td>
<p><code><a href="degCheckFactors.html">degCheckFactors()</a></code> </p>
</td>
<td><p>Distribution of gene ratios used to calculate Size Factors.</p></td>
</tr><tr>
<td>
<p><code><a href="degColors.html">degColors()</a></code> </p>
</td>
<td><p>Make nice colors for metadata</p></td>
</tr><tr>
<td>
<p><code><a href="degComps.html">degComps()</a></code> </p>
</td>
<td><p>Automatize the use of <code>results()</code> for multiple comparisons</p></td>
</tr><tr>
<td>
<p><code><a href="degCorCov.html">degCorCov()</a></code> </p>
</td>
<td><p>Calculate the correlation relationshipt among all covariates
in the metadata table</p></td>
</tr><tr>
<td>
<p><code><a href="degCovariates.html">degCovariates()</a></code> </p>
</td>
<td><p>Find correlation between pcs and covariates</p></td>
</tr><tr>
<td>
<p><code><a href="degDefault.html">degDefault()</a></code> <code><a href="degDefault.html">degCorrect()</a></code> </p>
</td>
<td><p>Method to get the default table to use.</p></td>
</tr><tr>
<td>
<p><code><a href="degFilter.html">degFilter()</a></code> </p>
</td>
<td><p>Filter genes by group</p></td>
</tr><tr>
<td>
<p><code><a href="degMA.html">degMA()</a></code> </p>
</td>
<td><p>MA-plot from base means and log fold changes</p></td>
</tr><tr>
<td>
<p><code><a href="degMB.html">degMB()</a></code> </p>
</td>
<td><p>Distribution of expression of DE genes compared to the background</p></td>
</tr><tr>
<td>
<p><code><a href="degMDS.html">degMDS()</a></code> </p>
</td>
<td><p>Plot MDS from normalized count data</p></td>
</tr><tr>
<td>
<p><code><a href="degMV.html">degMV()</a></code> </p>
</td>
<td><p>Correlation of the standard desviation and the mean of the abundance of a
set of genes.</p></td>
</tr><tr>
<td>
<p><code><a href="degMean.html">degMean()</a></code> </p>
</td>
<td><p>Distribution of pvalues by expression range</p></td>
</tr><tr>
<td>
<p><code><a href="degMerge.html">degMerge()</a></code> </p>
</td>
<td><p>Integrate data comming from degPattern into one data object</p></td>
</tr><tr>
<td>
<p><code><a href="degObj.html">degObj()</a></code> </p>
</td>
<td><p>Create a deg object that can be used to plot expression values
at shiny server:runGist(9930881)</p></td>
</tr><tr>
<td>
<p><code><a href="degPCA.html">degPCA()</a></code> </p>
</td>
<td><p>smart PCA from count matrix data</p></td>
</tr><tr>
<td>
<p><code><a href="degPatterns.html">degPatterns()</a></code> </p>
</td>
<td><p>Make groups of genes using expression profile.</p></td>
</tr><tr>
<td>
<p><code><a href="degPlot.html">degPlot()</a></code> </p>
</td>
<td><p>Plot top genes allowing more variables to color and shape points</p></td>
</tr><tr>
<td>
<p><code><a href="degPlotCluster.html">degPlotCluster()</a></code> </p>
</td>
<td><p>Plot clusters from degPattern function output</p></td>
</tr><tr>
<td>
<p><code><a href="degPlotWide.html">degPlotWide()</a></code> </p>
</td>
<td><p>Plot selected genes on a wide format</p></td>
</tr><tr>
<td>
<p><code><a href="degQC.html">degQC()</a></code> </p>
</td>
<td><p>Plot main figures showing p-values distribution and mean-variance correlation</p></td>
</tr><tr>
<td>
<p><code><a href="degResults.html">degResults()</a></code> </p>
</td>
<td><p>Complete report from DESeq2 analysis</p></td>
</tr><tr>
<td>
<p><code><a href="degSignature.html">degSignature()</a></code> </p>
</td>
<td><p>Plot gene signature for each group and signature</p></td>
</tr><tr>
<td>
<p><code><a href="degSummary.html">degSummary()</a></code> </p>
</td>
<td><p>Print Summary Statistics of Alpha Level Cutoffs</p></td>
</tr><tr>
<td>
<p><code><a href="degVB.html">degVB()</a></code> </p>
</td>
<td><p>Distribution of the standard desviation of
DE genes compared to the background</p></td>
</tr><tr>
<td>
<p><code><a href="degVar.html">degVar()</a></code> </p>
</td>
<td><p>Distribution of pvalues by standard desviation range</p></td>
</tr><tr>
<td>
<p><code><a href="degVolcano.html">degVolcano()</a></code> </p>
</td>
<td><p>Create volcano plot from log2FC and adjusted pvalues data frame</p></td>
</tr><tr>
<td>
<p><code><a href="geneInfo.html">geneInfo</a></code> </p>
</td>
<td><p>data.frame with chromose information for each gene</p></td>
</tr><tr>
<td>
<p><code><a href="geom_cor.html">geom_cor()</a></code> </p>
</td>
<td><p>Add correlation and p-value to a ggplot2 plot</p></td>
</tr><tr>
<td>
<p><code><a href="humanGender.html">humanGender</a></code> </p>
</td>
<td><p>DGEList object for DE genes betwen Male and Females</p></td>
</tr><tr>
<td>
<p><code><a href="significants.html">significants()</a></code> </p>
</td>
<td><p>Method to get the significant genes</p></td>
</tr>
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