# Reference

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