computeCoverage: Compute the coverage vector given a bamfile

Description Usage Arguments Value Author(s)

View source: R/coverage.R

Description

Compute the coverage vector given a bamfile

Usage

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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.