BamToBed: Convert bam format to bed format.

In esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

Description

This function convert a bam file into a bed file. Note:bed file is 0-based.

Usage

atacBam2Bed(atacProc, bamInput = NULL, bedOutput = NULL, ...)

## S4 method for signature 'ATACProc'
atacBam2Bed(atacProc, bamInput = NULL, bedOutput = NULL, ...)

bam2bed(bamInput, bedOutput = NULL, ...)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacBamSort, atacSam2Bam.
bamInput	Character scalar. Bam file input path.
bedOutput	Character scalar. Bed file output path. If ignored, bed file will be put in the same path as the bam file.
...	Additional arguments, currently unused.

Details

The bam file wiil be automatically obtained from object(atacProc) or input by hand. Output can be ignored.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Wei Zhang

See Also

atacBamSort atacSam2Bam

Examples

library(Rsamtools)
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
bam2bed(bamInput = ex1_file)

esATAC documentation built on Nov. 8, 2020, 6:58 p.m.