nucleR (version 2.4.0)

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

Arguments

ranges

Ranges to export, in IRanges, IRangesList or RangedData 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)

References

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

Examples

    ## Not run: 
#         # 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
#         # ...
#     ## End(Not run)