CutSitePre: Extract ATAC-seq cutting site from bed file.

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

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")

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.