UnzipAndMergeBed: Unzip all zipped BED files and merge them into one BED file

In enrichTF: Transcription Factors Enrichment Analysis

Description

This function process region BED files in three step: First, unzip the gzip and bzip2 BED input files. Second, select first 3 columns of the BED files. Third, merge the BED files into one BED.

Usage

enrichUnzipAndMergeBed(prevStep, bedInput = NULL, bedOutput = NULL, ...)

## S4 method for signature 'Step'
enrichUnzipAndMergeBed(prevStep, bedInput = NULL, bedOutput = NULL, ...)

unzipAndMergeBed(bedInput, bedOutput = NULL, ...)

Arguments

prevStep	Step-class object scalar. It needs to be the return value of upstream process from other packages, such as ATAC-seq peak calling result from esATAC.
bedInput	Character scalar or vector. The directory of region BED files for analysis. BED, BED.gz, BED.bz2 formats are supported.
bedOutput	Character scalar. The BED output file directory of merged BED files. Default: NULL (generated base on first BED file in bedInput)
...	Additional arguments, currently unused.

Details

All compressed files will be de-compressed. Only first 3 columns (chromasomes, start and end) will be collected. All BED files will be merged into one BED file.

Value

An invisible EnrichStep-class object (inherit from Step-class) scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

genBackground

Examples

foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed.gz")
gen <- unzipAndMergeBed(bedInput = foregroundBedPath)

enrichTF documentation built on Nov. 8, 2020, 6:15 p.m.