Count the number of reads in a given GRanges

Source: R/utils.R

Count the number of reads in a given GRanges

numReadsInBed(regions, bams = NA, countall = FALSE)

Arguments

regions

The GRanges object to count reads in.
bams

character. path to bam files from where the reads have to be counted
countall

logical. whether to keep both reads of paired-end data

Value

Total counts within given ranges per BAM file.