The countRangeset function is a convenience wrapper to perform read counting
iteratively over serveral range sets, here peak range sets. Internally,
the read counting is performed with the summarizeOverlaps function from the
GenomicAlignments package. The resulting count tables are directly saved to
files, one for each peak set.
library(GenomicRanges)
args <- systemArgs(sysma="param/count_rangesets.param", mytargets="targets_macs.txt")
args_bam <- systemArgs(sysma=NULL, mytargets="targets_bam.txt")
bfl <- BamFileList(outpaths(args_bam), yieldSize=50000, index=character())
countDFnames <- countRangeset(bfl, args, mode="Union", ignore.strand=TRUE)
writeTargetsout(x=args, file="targets_countDF.txt", overwrite=TRUE)