export.bed {nucleR} | R Documentation |
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 |
chrom |
For single |
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 # ...