importBed {AneuFinder} | 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

    importBed(bedfile, skip = 0, chromosome.format = "NCBI")

### Arguments

`bedfile` | Filename of the bed or bed.gz file.
`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 ...).

### Value

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

### Author(s)

Aaron Taudt

### Examples

    ## Get an example BED file with single-cell-sequencing reads
    bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData")
    ## Import the file and skip the first 10 lines
    data <- importBed(bedfile, skip=10)

[Package AneuFinder version 1.20.0 Index]