computeCoverage: Compute the coverage vector given a bamfile

In HTSeqGenie: A NGS analysis pipeline.

Description

Compute the coverage vector given a bamfile

Usage

computeCoverage(bamfile, extendReads = FALSE, paired_ends = FALSE,
  fragmentLength = NULL, maxFragmentLength = NULL)

Arguments

bamfile	A character string indicating the path of bam file
extendReads	A logical, indicating whether reads should be extended
paired_ends	A logical, indicating whether reads are paired
fragmentLength	An integer, indicating the new size of reads when extendReads is TRUE and paired_ends is FALSE. If NULL, read size is estimated using estimate.mean.fraglen from the chipseq package.
maxFragmentLength	An optional integer, specifying the maximal size of fragments. Longer fragments will be disregarded when computing coverage.

Value

A SimpleRleList object containing the coverage

Author(s)

Gregoire Pau

HTSeqGenie documentation built on Nov. 8, 2020, 6:12 p.m.