export.bed12: Export as bed12 format

In JokingHero/ORFik: Open Reading Frames in Genomics

Export as bed12 format

Description

bed format for multiple exons per group, as transcripts. Can be use as alternative as a sparse .gff format for ORFs. Can be direct input for ucsc browser or IGV

Usage

export.bed12(grl, file, rgb = 0)

Arguments

grl	A GRangesList
file	a character path to valid output file name
rgb	integer vector, default (0), either single integer or vector of same size as grl to specify groups. It is adviced to not use more than 8 different groups

Details

If grl has no names, groups will be named 1,2,3,4..

Value

NULL (File is saved as .bed)

See Also

Other utils: bedToGR(), convertToOneBasedRanges(), export.bigWig(), export.fstwig(), export.wiggle(), fimport(), findFa(), fread.bed(), optimizeReads(), readBam(), readBigWig(), readWig()

Examples

grl <- GRangesList(GRanges("1", c(1,3,5), "+"))
# export.bed12(grl, "output/path/orfs.bed")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.