systemPipeR (version 1.6.2)

countRangeset: Read counting for several range sets

Description

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.

Usage

countRangeset(bfl, args, format="tabular", ...)

Arguments

bfl

BamFileList object containing paths to one or more BAM files.

args

Object of class SYSargs where infile1(args) specifies the paths to the tabular range data files (e.g. peak ranges) used for counting.

format

Format of input range files. Currently, supported are tabular or bed. If tabular is selected then the input range files need to contain the proper column titles to coerce with as(..., "GRanges") to GRanges objects after importing them with read.delim. The latter is the case for the peak files (*peaks.xls) generated by the MACS2 software.

...

Arguments to be passed on to internally used summarizeOverlaps function.

Value

• Named character vector containing the paths from outpaths(args) to the resulting count table files.

See Also

summarizeOverlaps

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())

## 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)