\name{export.bed}
\alias{export.bed}
\alias{.export.bed}
\alias{export.bed,IRanges-method}
\alias{export.bed,CompressedIRangesList-method}
\alias{export.bed,RangedData-method}
\title{
	Export ranges in BED format
}
\description{
	Export ranges in BED format, compatible with UCSC genome browser, IGB, and others
}
\usage{
\S4method{export.bed}{IRanges}(ranges, score=NULL, chrom, name, desc=name, filepath=name)
\S4method{export.bed}{CompressedIRangesList}(ranges, score=NULL, name, desc=name, filepath=name, splitByChrom=TRUE)
\S4method{export.bed}{RangedData}(ranges, score=NULL, name, desc=name, filepath=name, splitByChrom=TRUE)
}
\arguments{
  \item{ranges}{
	Ranges to export, in \code{IRanges}, \code{IRangesList} or \code{RangedData} format
}
	\item{score}{
	Score data if not included in \code{ranges} object. Bed file will put all scores=1000 if scores are not present
}
	\item{chrom}{
	For single \code{IRanges} objects, the chromosome they represent. For other data types, values from \code{names(...)} will be used.
}
  \item{name}{
	Name of the track
}
  \item{desc}{
	Description of the track
}
	\item{filepath}{
	Path and prefix of the file(s) to write. Chromosome number and "bed" extension will be automatically added.
}
	\item{splitByChrom}{
	If multiple chromosomes are given, should they be splitted into one file per chromosome or shall them be saved all together?
}
}
\value{
	(none)
}
\references{
	BED format specification: http://genome.ucsc.edu/FAQ/FAQformat#format1
}
\author{
	Oscar Flores \email{oflores@mmb.pcb.ub.es}
}
\keyword{ file }
\examples{
	\dontrun{
		#Generate random ranges with scores
		ran = RangedData(IRanges(start=1:100, end=101:200), score=(1:100) / 100)	
		names(ran) = "chrX"
	
		#Export as bed file
		export.bed(ran, name="test_track", description="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
		# ...
	}
}