stopCodons {ORFik} | R Documentation |
In ATGTTTTGA, get the positions TGA. It takes care of exons boundaries, with exons < 3 length.
stopCodons(grl, is.sorted = FALSE)
grl |
a |
is.sorted |
a boolean, a speedup if you know the ranges are sorted |
a GRangesList of stop codons, since they might be split on exons
Other ORFHelpers:
defineTrailer()
,
longestORFs()
,
mapToGRanges()
,
orfID()
,
startCodons()
,
startSites()
,
stopSites()
,
txNames()
,
uniqueGroups()
,
uniqueOrder()
gr_plus <- GRanges(seqnames = c("chr1", "chr1"), ranges = IRanges(c(7, 14), width = 3), strand = c("+", "+")) gr_minus <- GRanges(seqnames = c("chr2", "chr2"), ranges = IRanges(c(4, 1), c(9, 3)), strand = c("-", "-")) grl <- GRangesList(tx1 = gr_plus, tx2 = gr_minus) stopCodons(grl, is.sorted = FALSE)