CutSitePre {esATAC} | R Documentation

## Extract ATAC-seq cutting site from bed file.

### Description

Extract cutting site from ATAC-seq fangment bed file (from `atacSamToBed`).

### Usage

    atacExtractCutSite(
      atacProc,
      bedInput = NULL,
      csOutput.dir = NULL,
      prefix = NULL,
      ...
    )

    ## S4 method for signature 'ATACProc'
    atacExtractCutSite(
      atacProc,
      bedInput = NULL,
      csOutput.dir = NULL,
      prefix = NULL,
      ...
    )

    extractcutsite(bedInput, csOutput.dir = NULL, prefix = NULL, ...)

### Arguments

`atacProc` | `ATACProc-class` object scalar. It has to be the return value of upstream process: `atacSamToBed`.
`bedInput` | `Character` scalar. Input bed file path, must be merged bed file(a line is a fragment). The input file should be UCSC bed format(0-based).
`csOutput.dir` | `Character` scalar. The output path, an empty folder would be great. Default: a folder in the same path as input bed file.
`prefix` | `Character` scalar. Output file name prefix, e.g. prefix_chr*.bed, default "Cutsite".
`...` | Additional arguments, currently unused.

### Details

In ATAC-seq data, every line in merged bed file (from `atacSamToBed`, the first 3 column is chr, start, end) means a DNA fragment, the cutting site is start+1 and end, this function extract and sort this information for the next step (`atacCutSiteCount`).

### Value

An invisible `ATACProc-class` object scalar for downstream analysis.

### Author(s)

Wei Zhang

### See Also

`atacCutSiteCount`

### Examples

    library(R.utils)
    fra_path <- system.file("extdata", "chr20.50000.bed.bz2", package="esATAC")
    frag <- as.vector(bunzip2(filename = fra_path,
    destname = file.path(getwd(), "chr20.50000.bed"),
    ext="bz2", FUN=bzfile, overwrite=TRUE, remove = FALSE))
    extractcutsite(bedInput = frag, prefix = "ATAC")

[Package esATAC version 1.12.0 Index]