SamToBam: Convert sam format to bam format.

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

Description

This function convert a sam file into a bam file.

Usage

atacSam2Bam(atacProc, samInput = NULL, bamOutput = NULL, ...)

## S4 method for signature 'ATACProc'
atacSam2Bam(atacProc, samInput = NULL, bamOutput = NULL, ...)

sam2bam(samInput, bamOutput = NULL, ...)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacBowtie2Mapping.
samInput	Character scalar. Sam file input path.
bamOutput	Character scalar. Bam file output path. If ignored, bed file will be put in the same path as the sam file.
...	Additional arguments, currently unused.

Details

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

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Wei Zhang

See Also

atacBowtie2Mapping atacBam2Bed atacBamSort

Examples

library(R.utils)
sam_bz <- system.file("extdata", "Example.sam.bz2", package="esATAC")
sam_path <- as.vector(bunzip2(filename = sam_bz,
destname = file.path(getwd(), "Example.sam"),
ext="bz2", FUN=bzfile, remove = FALSE))
sam2bam(samInput = sam_path)

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