ExomeDepth (version 0.9.2)

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, index = bam.file, granges, min.mapq = 1, read.width = 1)

Arguments

bam.file

BAM file to be parsed

index

Index of the BAM file, without the '.bai' suffix.

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.