PeakCallingMACS2: Use MACS2 to call peak

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

Use MACS2 to call peak

Description

Use MACS2 installed by to call peak

Usage

atacPeakCallingMACS2(
  atacProc,
  bedInput = NULL,
  background = NULL,
  outputPrefix = NULL,
  genomeSize = NULL,
  pvalueThreshold = 0.01,
  extsize = 150,
  shift = -round(extsize/2),
  ...
)

## S4 method for signature 'ATACProc'
atacPeakCallingMACS2(
  atacProc,
  bedInput = NULL,
  background = NULL,
  outputPrefix = NULL,
  genomeSize = NULL,
  pvalueThreshold = 0.01,
  extsize = 150,
  shift = -round(extsize/2),
  ...
)

peakCallingMACS2(
  bedInput,
  background = NULL,
  outputPrefix = NULL,
  genomeSize = NULL,
  pvalueThreshold = 0.01,
  extsize = 150,
  shift = -round(extsize/2),
  ...
)

testPeakCallingMACS2()

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacSamToBed, atacBedUtils.
bedInput	Character scalar. BED file input path.
background	Character scalar. background directory default: NULL (none)
outputPrefix	Character scalar. the output bed file path
extsize	Logical scalar. verbose output if TRUE.
shift	Character scalar. wg threshold set default: NULL (calculated)
...	Additional arguments, currently unused.
threshold	Numeric scalar. threshold (standard deviations) default: NULL (4.0)

Details

The parameter related to input and output file path will be automatically obtained from ATACProc-class object(atacProc) or generated based on known parameters if their values are default(e.g. NULL). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use peakCalling instead.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacSamToBed samToBed atacBedUtils bedUtils

Examples

library(R.utils)
library(magrittr)
td <- tempdir()
setTmpDir(td)

bedbzfile <- system.file(package="esATAC", "extdata", "chr20.50000.bed.bz2")
bedfile <- file.path(td,"chr20.50000.bed")
bunzip2(bedbzfile,destname=bedfile,overwrite=TRUE,remove=FALSE)

bedUtils(bedInput = bedfile,maxFragLen = 100, chrFilterList = NULL) %>%
atacPeakCalling

dir(td)

wzthu/esATAC documentation built on Aug. 12, 2022, 7:41 a.m.