BedToBigWig {esATAC} | R Documentation

## generate BigWig file from BED file

### Description

This function is used to generate BigWig file from BED reads file. The BigWig file can be shown reads coverage on genome browser.

### Usage

    atacBedToBigWig(
      atacProc,
      bedInput = NULL,
      bsgenome = NULL,
      bwOutput = NULL,
      toWig = FALSE,
      ...
    )

    ## S4 method for signature 'ATACProc'
    atacBedToBigWig(
      atacProc,
      bedInput = NULL,
      bsgenome = NULL,
      bwOutput = NULL,
      toWig = FALSE,
      ...
    )

    bedToBigWig(bedInput, bsgenome = NULL, bwOutput = NULL, toWig = FALSE, ...)

### 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.
`bsgenome` | `BSGenome` object scalar. BSGenome object for specific species.
`bwOutput` | `Character` scalar. BigWig file output path.
`toWig` | `Logical` scalar.
`...` | Additional arguments, currently unused. Save as wig file instead of binary BigWig file

### 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 `bedToBigWig` 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()
    setTmpDir(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)

    library(BSgenome.Hsapiens.UCSC.hg19)
    bedToBigWig(bedfile, BSgenome.Hsapiens.UCSC.hg19)

    dir(td)

    ## End(Not run)

[Package esATAC version 1.14.0 Index]