readGFBed: Read genomic feature bed file

Description Usage Arguments Value Author(s) Examples

View source: R/HiCglmiMiscFun.R

Description

Function to import a genomic feature bed file. The bed file must contain coordinates of the genomic features. It can be for instance ChIP-seq peak coordinates or functional element coordinates.

Usage

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readGFBed(GFBedFile, seqInfoChr)

Arguments

GFBedFile

The name of the bed file. If it does not contain an absolute path, the file name is relative to the current working directory.

seqInfoChr

A Seqinfo object for the corresponding genome.

Value

A GRanges object is returned.

Author(s)

Raphael Mourad

Examples

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bed_file <- system.file("inst/extdata", "BEAF32_Kc167_CS_dm3.bed", package="HiCfeat")
data(dataExample)
seqInfoChr=dataExample$SeqInfoChr
GFBed=readGFBed(bed_file,seqInfoChr)

HiCglmi documentation built on April 19, 2018, 1:04 a.m.