PeakCallingFseq {esATAC} | R Documentation

## 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)

[Package esATAC version 1.14.0 Index]