readBed: Read a BED file and convert it to GRanges.

Description Usage Arguments Value Examples

View source: R/readData.R

Description

The function reads a BED file that contains location and other information on genomic features and returns a GRanges object. The minimal information that the BED file has to have is chromosome, start and end columns. it can handle all BED formats up to 12 columns.

Usage

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readBed(file, track.line = FALSE, remove.unusual = FALSE,
  zero.based = TRUE)

Arguments

file

location of the file, a character string such as: "/home/user/my.bed" or the input itself as a string (containing at least one \n). The file can end in .gz, .bz2, .xz, or .zip and/or start with http:// or ftp://. If the file is not compressed it can also start with https:// or ftps://.

track.line

the number of track lines to skip, "auto" to detect them automatically or FALSE(default) if the bed file doesn't have track lines

remove.unusual

if TRUE remove the chromosomes with unsual names, such as chrX_random (Default:FALSE)

zero.based

a boolean which tells whether the ranges in the bed file are 0 or 1 base encoded. (Default: TRUE)

Value

GRanges object

Examples

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my.file=system.file("extdata","chr21.refseq.hg19.bed",package="genomation")
refseq = readBed(my.file,track.line=FALSE,remove.unusual=FALSE)
head(refseq)

BIMSBbioinfo/genomation documentation built on Feb. 4, 2018, 12:11 p.m.