runDiff: Differential abundance analysis for many range sets
In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description Usage Arguments Value Author(s) See Also Examples

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.

1	runDiff(args, diffFct, targets, cmp, dbrfilter, ...)

`args`	Object of class `SYSargs` or `SYSargs2` where `infile1(args)` specifies the paths to the tabular read count data files and `outputs` files to the result files.
`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`	`character 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.

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.

Thomas Girke

run_edgeR, run_DESeq2, filterDEGs

## 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)