FragLenDistr {esATAC} | R Documentation

## Quality control for fragment length distribution

### Description

These functions are used to generate fragment distribution plot. The fourier transform of fragment distribution will be calculated. Strength distribution around period at 10.4bp and 180bp will be shown in another two plots.

### Usage

    atacFragLenDistr(atacProc, reportPrefix = NULL, bedInput = NULL, ...)

    ## S4 method for signature 'ATACProc'
    atacFragLenDistr(atacProc, reportPrefix = NULL,
      bedInput = NULL, ...)

    fragLenDistr(bedInput, reportPrefix = NULL, ...)

### Arguments

`atacProc` | `ATACProc-class` object scalar. It has to be the return value of upstream process: `atacSamToBed` `samToBed` `atacBedUtils` `bedUtils`
`reportPrefix` | `Character` scalar. The prefix of report files path.
`bedInput` | `Character` scalar. BED file input path.
`...` | 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 `fragLenDistr` 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)
    td <- tempdir()
    options(atacConf=setConfigure("tmpdir",td))

    bedbzfile <- system.file(package="esATAC", "extdata", "chr20.50000.bed.bz2")
    bedfile <- file.path(td,"chr20.50000.bed")
    ## Not run:
    bunzip2(bedbzfile,destname=bedfile,overwrite=TRUE,remove=FALSE)
    fragLenDistr(bedfile)

    ## End(Not run)

    dir(td)

[Package esATAC version 1.6.1 Index]