export.bed {nucleR} | R Documentation

## Export ranges in BED format

### Description

Export ranges in BED format, compatible with UCSC genome browser, IGB, and others.

### Usage

    export.bed(
      ranges,
      score = NULL,
      chrom,
      name,
      desc = name,
      filepath = name,
      splitByChrom = TRUE
    )

    ## S4 method for signature 'IRanges'
    export.bed(ranges, score = NULL, chrom, name, desc = name, filepath = name)

    ## S4 method for signature 'CompressedIRangesList'
    export.bed(
      ranges,
      score = NULL,
      name,
      desc = name,
      filepath = name,
      splitByChrom = TRUE
    )

    ## S4 method for signature 'GRanges'
    export.bed(
      ranges,
      score = NULL,
      name,
      desc = name,
      filepath = name,
      splitByChrom = TRUE
    )

### Arguments

`ranges` | Ranges to export, in IRanges::IRanges, IRanges::IRangesList or GenomicRanges::GRanges format
`score` | Score data if not included in `ranges` object. Bed file will put all scores=1000 if scores are not present
`chrom` | For single `IRanges` objects, the chromosome they represent. For other data types, values from `names(...)` will be used.
`name` | Name of the track
`desc` | Description of the track
`filepath` | Path and prefix of the file(s) to write. Chromosome number and "bed" extension will be automatically added.
`splitByChrom` | If multiple chromosomes are given, should they be splitted into one file per chromosome or shall them be saved all together?

### Value

(none)

### Author(s)

Oscar Flores oflores@mmb.pcb.ub.es

### References

BED format specification: http://genome.ucsc.edu/FAQ/FAQformat#format1

### Examples

    # Generate some ranges with scores
    library(GenomicRanges)
    ran <- GRanges(
        seqnames="chrX", ranges=IRanges(start=1:100, end=101:200),
        score=(1:100)/100
    )

    # Export as bed file
    export.bed(ran, name="test_track", desc="Just a test track")

    # If executed, this would create a file named "test_track.chrX.bed" with:

    #    track name="test_track" description="Just a test track" useScore=0
    # chrX    1 101 nucl1 0.01
    # chrX    2 102 nucl2 0.02
    # chrX    3 103 nucl3 0.03
    # ...

[Package nucleR version 2.24.0 Index]