readCustomBedFile {chromstaR} | R Documentation

## Read bed-file into GRanges

### 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)

[Package chromstaR version 1.14.1 Index]