countReads-methods {GreyListChIP} | R Documentation |
BamFile
Given the tiling of the genome created when the GreyList
object was created (or replaced via getKaryotype
), count reads
overlapping the bins, in preparation for estimating the threshold for
grey-listing bins.
countReads(obj,bamFile)
obj |
A |
bamFile |
A |
This method counts reads contained within the bins that make up the genome tiling. Bins are overlapping (by default 1Kb bins at 512b intervals) so reads are counted once for each bin that wholly contains them.
The modified GreyList
object, with added counts.
Gord Brown
# Load a pre-built GreyList object. data(greyList) path <- system.file("extra", package="GreyListChIP") ## Not run: fn <- file.path(path,"sample_chr21.bam") ## Not run: gl <- countReads(gl,fn)