coverageBamInGRanges: Coverage profile from a bam file across genomic ranges

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

Description

Coverage profile from a bam file across genomic ranges

Usage

coverageBamInGRanges(bam.file, granges, min.mapq = NULL,
  reads.collapsed = FALSE, width = NULL)

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. Note: all ranges must be of the same width
min.mapq	minimal mapping quality. Default is to ignore mapping quality
reads.collapsed	logical indicating whether duplicated reads were removed and counts were added as _x to the readnames (this is the case for some of the tools from the Rajewski lab)
width	length of the sequencing reads, by default this will be extracted from the bam file

Value

count matrix with rows for each element of the GRanges object

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