readGFBed: Read genomic feature bed file

In HiCfeat: Multiple Logistic Regression for 3D Chromatin Domain Border Analysis

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

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

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

HiCfeat documentation built on May 2, 2019, 2:11 a.m.