countRangeset {systemPipeR} | R Documentation |
Convenience function to perform read counting iteratively for serveral range sets, e.g. peak range sets or feature types. Internally, the read counting
is performed with the summarizeOverlaps
function from the GenomicAlignments
package. The resulting count tables are directly saved to files.
countRangeset(bfl, args, format="tabular", ...)
bfl |
|
args |
Object of class |
format |
Format of input range files. Currently, supported are |
... |
Arguments to be passed on to internally used |
Named character vector containing the paths from outpaths(args)
to the
resulting count table files.
Thomas Girke
summarizeOverlaps
## 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) ## End(Not run)