methylKit (version 0.99.2)

readBed: read a bed file and convert it to GRanges

Description

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

Usage

readBed(location,remove.unsual=TRUE)
# S4 method for character
readBed(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 chromosomes etc

Value

GRanges object

Examples

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

# }