# Report of DEG analysis

## Documentation for package ‘DEGreport’ version 1.42.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

DEGreport-package | Deprecated functions in package DEGreport
as.DEGSet | DEGSet
as.DEGSet-method | DEGSet
createReport | Create report of RNAseq DEG anlaysis
deg | Method to get all table stored for an specific comparison
deg-method | 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
degCorrect | Method to get the default table to use.
degCorrect-method | Method to get the default table to use.
degCovariates | Find correlation between pcs and covariates
degDefault | Method to get the default table to use.
degDefault-method | 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
degMean | Distribution of pvalues by expression range
degMerge | Integrate data comming from degPattern into one data object
degMV | Correlation of the standard desviation and the mean of the abundance of a set of genes.
degObj | Create a deg object that can be used to plot expression values at shiny server:runGist(9930881)
degPatterns | Make groups of genes using expression profile.
degPCA | smart PCA from count matrix data
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
DEGreport | Deprecated functions in package DEGreport
degResults | Complete report from DESeq2 analysis
DEGSet | DEGSet
DEGSet-class | DEGSet
degSignature | Plot gene signature for each group and signature
degSummary | Print Summary Statistics of Alpha Level Cutoffs
degVar | Distribution of pvalues by standard desviation range
degVB | Distribution of the standard desviation of DE genes compared to the background
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
significants-method | Method to get the significant genes