Rsortbam {esATAC} | R 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)

[Package esATAC version 1.12.0 Index]