countBamInGRanges: Count reads from a bam file in genomic ranges

Description Usage Arguments Value

View source: R/gff.R

Description

Count reads from a bam file in genomic ranges

Usage

1
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, 2017, 11:03 p.m.