countBamInGRanges.exomeDepth: Compute read count data from BAM files.
Description
Parses a BAM file and count reads that are located within a target
region defined by a GenomicRanges object.Usage
countBamInGRanges.exomeDepth(bam.file, granges, min.mapq = 1, read.width = 1)
Arguments
bam.file
BAM file to be parsed
granges
Genomic ranges object defining the bins
min.mapq
Minimum mapping quality
read.width
Window around the target region to count a read
within the bin
Value
- A GRanges object with count data.
Details
Largely derived from its equivalent function in the exomeCopy package.