filterDEGs: Filter and plot DEG results

In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

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, while 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.

Details

Currently, there is no community standard available how to calculate fold changes (here logFC) of genomic ranges, such as gene or feature ranges, to unambiguously refer to them as features with increased or decreased read abundandce; or in case of gene expression experiments to up or down regulated genes, respectively. To be consistent within systemPipeR, the corresponding functions, such as filterDEGs, use here the following definition. Genomic ranges with positive logFC values are classified as up and those with negative logFC values as down. This means if a comparison among two samples a and b is specified in the corresponding targets file as a-b then the feature with a positive logFC has a higher _normalized_ read count value in sample a than in sample b, and vice versa. To inverse this assignment, users want to change the specification of their chosen sample comparison(s) in the targets file accordingly, e.g. change a-b to b-a. Alternatively, one can swap the column order of the matrix assigned to the cmp argument of the run_edgeR or run_DESeq2 functions. Users should also be aware that for logFC values close to zero (noise range), the direction of the fold change (sign of logFC) can be very sensitive to minor differences in the normalization method, while this assignment is much more robust for more pronounced changes or higher absolute logFC values.

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.

Author(s)

Thomas Girke

See Also

run_edgeR

Examples

targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
targets <- read.delim(targetspath, comment.char = "#")
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

tgirke/systemPipeR documentation built on Sept. 24, 2024, 9:48 a.m.