read.bed-methods: read a bed file and convert it to GRanges

In fortunatobianconi/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

The function reads a BED file and coverts it to a GRanges object

Usage

  read.bed(location,remove.unsual=TRUE)

Arguments

location	location of the file, a character string such as: "/home/user/my.bed"
remove.unsual	if TRUE(default) remove the chromomesomes with unsual names, mainly random chromsomes etc

Value

GRanges object

Note

one bed track per file is only accepted, the bed files with multiple tracks will cause an error

Examples

bed.file=system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit")
bed.gr=read.bed(location=bed.file,remove.unsual=TRUE)

fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.