importBed {RCAS} | R Documentation

## importBed

### Description

This function uses `rtracklayer::import.bed()` function to import BED files

### Usage

    importBed(filePath, sampleN = 0, keepStandardChr = TRUE,
      debug = TRUE, ...)

### Arguments

`filePath` | Path to a BED file
`sampleN` | A positive integer value. The number of intervals in the input BED file are randomly downsampled to include intervals as many as `sampleN`. The input will be downsampled only if this value is larger than zero and less than the total number of input intervals.
`keepStandardChr` | TRUE/FALSE (default:TRUE). If set to TRUE, will convert the `seqlevelsStyle` to 'UCSC' and apply `keepStandardChromosomes` function to only keep data from the standard chromosomes
`debug` | TRUE/FALSE (default:TRUE). Set to FALSE to turn off messages
`...` | Other arguments passed to rtracklayer::import.bed function

### Value

A `GRanges` object containing the coordinates of the intervals from an input BED file

### Examples

    input <- system.file("extdata", "testfile.bed", package='RCAS')
    importBed(filePath = input, keepStandardChr = TRUE)

[Package RCAS version 1.12.0 Index]