runDiff: Differential abundance analysis for many range sets

View source: R/chipseq.R

runDiffR Documentation

Differential abundance analysis for many range sets

Description

Convenience wrapper function for run_edgeR and run_DESeq2 to perform differential expression or abundance analysis iteratively for several count tables. The latter can be peak calling results for several samples or counts generated for different genomic feature types. The function also returns the filtering results and plots from filterDEGs.

Usage

runDiff(args, outfiles=NULL, diffFct, targets, cmp, dbrfilter, ...)

Arguments

args

An instance of SYSargs or SYSargs2 constructed from a targets file where the first column (targetsin(args) or targets.as.df(targets(args))) contains the paths to the tabular read count data files. Another possibily is named character vector with the paths to the tabular range data files and the elements names should be the sampleID.

outfiles

Default is NULL. When args is an object of named character vector class, outfile argument is required. Named character vector with the paths to the resulting count tables and the elements names should be the sampleID.

diffFct

Defines which function should be used for the differential abundance analysis. Can be diffFct=run_edgeR or diffFct=run_DESeq2.

targets

targets data.frame

cmp

codecharacter matrix where comparisons are defined in two columns. This matrix should be generated with readComp() from the targets file. Values used for comparisons need to match those in the Factor column of the targets file.

dbrfilter

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. Those values are passed on to the filterDEGs function.

...

Arguments to be passed on to the internally used run_edgeR or run_DESeq2 function.

Value

Returns list containing the filterDEGs results for each count table. Each result set is a list with four components which are described under ?filterDEGs. The result files contain the edgeR or DESeq2 results from the comparisons specified under cmp. The base names of the result files are the same as the corresponding input files specified under countfiles and the value of extension appended.

Author(s)

Thomas Girke

See Also

run_edgeR, run_DESeq2, filterDEGs

Examples

## Paths to BAM files
param <- system.file("extdata", "bowtieSE.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args_bam <- systemArgs(sysma=param, mytargets=targets)
bfl <- BamFileList(outpaths(args_bam), yieldSize=50000, index=character())

## Not run: 
## SYSargs with paths to range data and count files
args <- systemArgs(sysma="param/count_rangesets.param", mytargets="targets_macs.txt")

## Iterative read counting
countDFnames <- countRangeset(bfl, args, mode="Union", ignore.strand=TRUE)
writeTargetsout(x=args, file="targets_countDF.txt", overwrite=TRUE)

## Run differential abundance analysis
cmp <- readComp(file=args_bam, format="matrix")
args_diff <- systemArgs(sysma="param/rundiff.param", mytargets="targets_countDF.txt")
dbrlist <- runDiff(args, diffFct=run_edgeR, targets=targetsin(args_bam), cmp=cmp[[1]], independent=TRUE, dbrfilter=c(Fold=2, FDR=1))
writeTargetsout(x=args_diff, file="targets_rundiff.txt", overwrite=TRUE)

## End(Not run)

tgirke/systemPipeR documentation built on Aug. 30, 2022, 10 p.m.