longestORFs: Get longest ORF per stop site

In JokingHero/ORFik: Open Reading Frames in Genomics

Get longest ORF per stop site

Description

Rule: if seqname, strand and stop site is equal, take longest one. Else keep. If IRangesList or IRanges, seqnames are groups, if GRanges or GRangesList seqnames are the seqlevels (e.g. chromosomes/transcripts)

Usage

longestORFs(grl)

Arguments

grl	a GRangesList/IRangesList, GRanges/IRanges of ORFs

Value

a GRangesList/IRangesList, GRanges/IRanges (same as input)

See Also

Other ORFHelpers: defineTrailer(), mapToGRanges(), orfID(), startCodons(), startSites(), stopCodons(), stopSites(), txNames(), uniqueGroups(), uniqueOrder()

Examples

ORF1 = GRanges("1", IRanges(10,21), "+")
ORF2 = GRanges("1", IRanges(1,21), "+") # <- longest
grl <- GRangesList(ORF1 = ORF1, ORF2 = ORF2)
longestORFs(grl) # get only longest

JokingHero/ORFik documentation built on Oct. 21, 2024, 11:42 a.m.