All functions

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.

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.

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-package

Deprecated functions in package DEGreport

degResults

Complete report from DESeq2 analysis

DEGSet DEGSetFromEdgeR DEGSetFromDESeq2

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

significants

Method to get the significant genes