Rsortbam: Sort bam file and rebuild bai index.

RsortbamR Documentation

Sort bam file and rebuild bai index.

Description

Sort bamfile and build index.

Usage

atacBamSort(atacProc, bamInput = NULL, bamOutput = NULL, ...)

## S4 method for signature 'ATACProc'
atacBamSort(atacProc, bamInput = NULL, bamOutput = NULL, ...)

bamsort(bamInput = NULL, bamOutput = NULL, ...)

Arguments

atacProc

ATACProc-class object scalar. It has to be the return value of upstream process: atacSam2Bam.

bamInput

Character scalar. Input bam file path.

bamOutput

Character scalar. Output bam file path.

...

Additional arguments, currently unused.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Wei Zhang

See Also

atacSam2Bam atacBam2Bed

Examples


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


wzthu/wzzw documentation built on Aug. 13, 2022, 7:11 a.m.