export.bed: Export ranges in BED format

In gthar/nucleR: Nucleosome positioning package for R

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)

## S4 method for signature 'RangedData'
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 [e-mail]

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
# ...

gthar/nucleR documentation built on May 28, 2019, 4:37 p.m.