export.bed: Export ranges in BED format
In gthar/nucleR2: Nucleosome positioning package for R

Description Usage Arguments Value Author(s) References Examples

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

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)

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

`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?

(none)

Oscar Flores oflores@mmb.pcb.ub.es

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

# 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
# ...