PeakCallingFseq: Use F-seq to call peak

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

Use F-seq to call peak

Description

Use F-seq to call peak

Usage

atacPeakCalling(
  atacProc,
  bedInput = NULL,
  background = NULL,
  genomicReadsCount = NULL,
  fragmentSize = 0,
  featureLength = NULL,
  bedOutput = NULL,
  ploidyDir = NULL,
  fileformat = c("bed", "wig", "npf"),
  wiggleTrackStep = NULL,
  threshold = NULL,
  verbose = TRUE,
  wgThresholdSet = NULL,
  ...
)

## S4 method for signature 'ATACProc'
atacPeakCalling(
  atacProc,
  bedInput = NULL,
  background = NULL,
  genomicReadsCount = NULL,
  fragmentSize = 0,
  featureLength = NULL,
  bedOutput = NULL,
  ploidyDir = NULL,
  fileformat = c("bed", "wig", "npf"),
  wiggleTrackStep = NULL,
  threshold = NULL,
  verbose = TRUE,
  wgThresholdSet = NULL,
  ...
)

peakCalling(
  bedInput,
  background = NULL,
  genomicReadsCount = NULL,
  fragmentSize = 0,
  featureLength = NULL,
  bedOutput = NULL,
  ploidyDir = NULL,
  fileformat = c("bed", "wig", "npf"),
  wiggleTrackStep = NULL,
  threshold = NULL,
  verbose = TRUE,
  wgThresholdSet = NULL,
  ...
)

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)
genomicReadsCount	Integer scalar. genomic count of sequence reads. default: NULL (calculated)
fragmentSize	Integer scalar. fragment size. set NULL to estimat from data. default:0
featureLength	Character scalar. feature length default: NULL (600)
bedOutput	Character scalar. the output bed file path
ploidyDir	Character scalar. ploidy/input directory. default: NULL
fileformat	Character scalar. File format of result. default: bed
wiggleTrackStep	Integer scalar. wiggle track step default: NULL (1)
threshold	Numeric scalar. threshold (standard deviations) default: NULL (4.0)
verbose	Logical scalar. verbose output if TRUE.
wgThresholdSet	Character scalar. wg threshold set default: NULL (calculated)
...	Additional arguments, currently unused.

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/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.