# Report of DEG analysis

## Documentation for package ‘DEGreport’ version 1.16.0

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

## Help Pages

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
deg-method | Method to get all table stored for an specific comparison
degCheckFactors | Distribution of gene ratios used to calculate Size Factors.
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 | Method to get the default table to use.
degDefault-method | Method to get the default table to use.
degFilter | Filter genes by group
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. Note that this function doesn't calculate significant difference between groups, so the matrix used as input should be already filtered to contain only genes that are significantly different.
degPCA | smart PCA from count matrix data
degPlot | Plot top genes allowing more variables to color and shape points
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
DEGSetFromDESeq2 | DEGSet
DEGSetFromDESeq2-method | DEGSet
DEGSetFromEdgeR | DEGSet
DEGSetFromEdgeR-method | 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
plotMA | MA-plot from base means and log fold changes
plotMA-method | MA-plot from base means and log fold changes
significants | Method to get the significant genes
significants-method | Method to get the significant genes