readBed2: Read a bed file to genomicRanges Object with option for...

In kevincjnixon/ChIPATAC: Wrapper functions for useful genomic analyses like ChIP-seq or ATAC-seq.

Read a bed file to genomicRanges Object with option for seqlengths

Description

Read a bed file to genomicRanges Object with option for seqlengths

Usage

readBed2(filename, HOCO = F, species = "human", BSg = NULL)

Arguments

filename	Character of .bed file name and location (assumes no header)
HOCO	Boolean indicaitng if .bed file is HOCOMOCO TFBS bed file. Default is FALSE
species	One of "human" or "mouse" to use already specified BSgenome objects. Leave NULL to use custom BSgenome.
BSg	BSgenome object containign seqlengths for genome of interest. Use if you want to specify specific BSgenome (especially if not mouse or human). Or leave NULL along with 'species' to not include seqlengths.

Value

GRanges object of bedfile regions

kevincjnixon/ChIPATAC documentation built on May 25, 2023, 9:33 p.m.