countBamInGRanges: Count reads from a bam file in genomic ranges

In matthiasheinig/seqQTL: Package for preprocessing sequencing based traits for QTL analysis

Description

Count reads from a bam file in genomic ranges

Usage

countBamInGRanges(bam.file, granges, min.mapq = NULL, read.width = 1)

Arguments

bam.file	filename of the bam file. The bam file must be sorted and indexed
granges	GRanges object in which to count the reads
min.mapq	minimal mapping quality. Default is to ignore mapping quality
read.width	the length of a read to be used for overlaps. Default is to #' use just the start position of the read.

Value

count vector of the same length as the GRanges object

matthiasheinig/seqQTL documentation built on May 21, 2019, 1:16 p.m.