readCustomBedFile: Read bed-file into GRanges

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

This is a simple convenience function to read a bed(.gz)-file into a GRanges-class object. The bed-file is expected to have the following fields: chromosome, start, end, name, score, strand.

Usage

readCustomBedFile(
  bedfile,
  col.names = c("chromosome", "start", "end", "name", "score", "strand"),
  col.classes = NULL,
  skip = 0,
  chromosome.format = "NCBI",
  sep = ""
)

Arguments

bedfile	Filename of the bed or bed.gz file.
col.names	A character vector giving the names of the columns in the bedfile. Must contain at least c('chromosome','start','end').
col.classes	A character vector giving the classes of the columns in bedfile. Speeds up the import.
skip	Number of lines to skip at the beginning.
chromosome.format	Desired format of the chromosomes. Either 'NCBI' for (1,2,3 ...) or 'UCSC' for (chr1,chr2,chr3 ...) or NULL to keep the original names.
sep	Field separator from read.table.

Value

A GRanges-class object with the contents of the bed-file.

Author(s)

Aaron Taudt

Examples

## Get an example BED file
bedfile <- system.file("extdata", "liver-H3K4me3-BN-male-bio2-tech1.bed.gz",
                       package="chromstaRData")
## Import the file and skip the first 10 lines
data <- readCustomBedFile(bedfile, skip=10)

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.