systemPipeR (version 1.0.12)

filterDEGs: Filter and plot DEG results

Description

Filters and plots DEG results for a given set of sample comparisons. The gene idenifiers of all (i) Up_or_Down, (ii) Up and (iii) Down regulated genes are stored as separate list components and the corresponding summary statistics, stored in a fourth list component, is plotted in form of a stacked bar plot.

Usage

filterDEGs(degDF, filter, plot = TRUE)

Arguments

degDF

data.frame generated by run_edgeR

filter

Named vector with filter cutoffs of format c(Fold=2, FDR=1) where Fold refers to the fold change cutoff (unlogged) and FDR to the p-value cutoff.

plot

Allows to turn plotting behavior on and off with default set to TRUE.

Value

Returns list with four components

UporDown

List of up or down regulated gene/transcript indentifiers meeting the chosen filter settings for all comparisons defined in data frames pval and log2FC.

Up

Same as above but only for up regulated genes/transcript.

Down

Same as above but only for down regulated genes/transcript.

See Also

run_edgeR

Examples

targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
targets <- read.delim(targetspath, comment="#")
cmp <- readComp(file=targetspath, format="matrix", delim="-")
countfile <- system.file("extdata", "countDFeByg.xls", package="systemPipeR")
countDF <- read.delim(countfile, row.names=1)
edgeDF <- run_edgeR(countDF=countDF, targets=targets, cmp=cmp[[1]], independent=FALSE, mdsplot="")
pval <- edgeDF[, grep("_FDR$", colnames(edgeDF)), drop=FALSE]
fold <- edgeDF[, grep("_logFC$", colnames(edgeDF)), drop=FALSE]
DEG_list <- filterDEGs(degDF=edgeDF, filter=c(Fold=2, FDR=10))
names(DEG_list)
DEG_list$Summary