atacPairedEnd: pull in (filter and assemble as an object) some or all of the...

In RamsinghLab/ATACseeker: Utilities for ATACseq QC, differential accessibility, and integration

Description

pull in (filter and assemble as an object) some or all of the "useful" reads in a paired-end ATACseq run (i.e., the majority of ATACseq studies)

Usage

atacPairedEnd(bam, genome = c("hg19", "mm10"), bamParams = NULL,
  which = NULL, ...)

Arguments

bam	character string, the BAM file to parse
genome	optional character string, the genome assembly to target
bamParams	optional any parameters to pass through to ScanBamParam
which	optional a GRanges object with specific regions to extract

Value

a GenomicAlignmentPairs object

Examples

## Not run: 

data(cytobands_hg19)
del7q <- byBand(cytobands_hg19)$chr7q22.1
galp <- atacPairedEnd('chr7.q10.CD49f_r1.hg19.bam', which=del7q)

library(Mus.musculus)
SMO <- transcriptsBy(Mus.musculus, 'gene')[['319757']]
galp <- atacPairedEnd('A1.SMO.bam', which=SMO)

library(Mus.musculus)
chr6 <- GRanges('chr6', IRanges(1, seqlengths(Mus.musculus)['chr6']), '*')
galp <- atacPairedEnd("A2.mm10.unique.bam",
                      bamParams=properPairedEndAtacFilters(which=chr6))

## End(Not run)

RamsinghLab/ATACseeker documentation built on May 8, 2019, 8:05 a.m.