methylKit (version 0.9.5)

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

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

Examples

# NOT RUN {
bed.file=system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit")
bed.gr=read.bed(location=bed.file,remove.unsual=TRUE)
# }