BedToBigWig: generate BigWig file from BED file

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

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)

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.