bam2coverage: Convert a bam file to coverage

In musikutiv/tsTools: Toolbox for Functional Genomics Data Processing in R

Convert a bam file to coverage

Description

Reads can optionally be filtered by a chromosome inclusion list Single reads will be extended to the provided fragment length

Usage

bam2coverage(file.id, type = c("SINGLE", "PAIRED"), fragment.length = 200,
  chr.flt = NA)

Arguments

file.id	path of the bam file
type	sequencing library type "SINGLE" or "PAIRED"
fragment.length	average chromatin fragment size, default 200
chr.flt	vector of chromosome names to be included

Value

a coverage object (RleList as returned by coverage)

musikutiv/tsTools documentation built on July 25, 2024, 2:42 a.m.