bam2counts: Compute the number of reads fall into specific genomic region
Description
bam2counts computes the number of reads fall into specific genomic
region such as promoter, enhancer, genebody
Usage
bam2counts(bamFile, region, fragLength = 180)
Arguments
bamFile
Aligned bam file as input.
region
The GRanges object defined by user to calculate the number of reads fall into
this specific region. For ChIP-Seq of histone modifications they are usually
promoter, enhancer and genebody regions.
fragLength
Extend reads toward the 3'-end to the average DNA fragment size obtained
after DNA size selection