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

Description Usage Arguments Value Note Examples

Description

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

Usage

1
  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

1
2
bed.file=system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit")
bed.gr=read.bed(location=bed.file,remove.unsual=TRUE)

tectronics/methylkit documentation built on May 27, 2017, 4:14 a.m.