This function takes in a list of bam files and creates a binned
counts file. If a mask file is provided, it will also create
a masked binned counts file. The output file is comma separated and
the first column is the sampleID, the header is the chromosome name of
each bin.
Usage
makeBinnedCountsFile(bam.file.list, sampleIDs, binned.counts.fname, mask = NULL, k = 20000)
Arguments
bam.file.list
list of bam file names
sampleIDs
list of sampleIDs, assumed to be in the same order as
the bam files in bam.file.list
binned.counts.fname
file name of the output binned counts file
mask
file name of a bed file with the regions to be masked out. Default
is no mask file