BedCheck: Performs checks un cleanups on a WES capture bed file

In gustaveroussy/EaCoN: EaCoN : Easy Copy Number !

Description

This function cleans (when necessary) a BED file by detecting and merging overlapped regions and sorting by chr > start > end.

Usage

EaCoN.BedCheck(bed.file = NULL, genome.pkg = "BSgenome.Hsapiens.UCSC.hg19",
out.dir = getwd(), return.data = FALSE)

Arguments

bed.file	BED File corresponding to the captured genomic regions in the WES experiment (usually given by the manufacturer.
genome.pkg	Name of the BSgenome package corresponding to the genome used to map the BAM files.
out.dir	Output directory.
return.data	Return the checked / cleaned BED as a data.frame (and still write it as a BED file).

Details

Only genomes available in the chomosomes data package are compatible with this function.

Value

Checked / cleaned BED is written in out.dir, and returned as a data.frame if return.data is set to TRUE.

Author(s)

Bastien Job

gustaveroussy/EaCoN documentation built on Oct. 20, 2021, 2:41 a.m.