txNames {ORFik} | R Documentation |
Using the ORFik definition of orf name, which is: example ENSEMBL: tx name: ENST0909090909090 orf id: _1 (the first of on that tx) orf_name: ENST0909090909090_1 So therefor txNames("ENST0909090909090_1") = ENST0909090909090
txNames(grl, ref = NULL, unique = FALSE)
grl |
a |
ref |
a reference |
unique |
a boolean, if true unique the names, used if several orfs map to same transcript and you only want the unique groups |
The names must be extracted from a column called names, or the names of the grl object. If it is already tx names, it returns the input
NOTE! Do not use _123 etc in end of transcript names if it is not ORFs. Else you will get errors. Just _ will work, but if transcripts are called ENST_123124124000 etc, it will crash, so substitute "_" with "." gsub("_", ".", names)
a character vector of transcript names, without _* naming
Other ORFHelpers:
defineTrailer()
,
longestORFs()
,
mapToGRanges()
,
orfID()
,
startCodons()
,
startSites()
,
stopCodons()
,
stopSites()
,
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_1 = gr_plus, tx2_1 = gr_minus) # there are 2 orfs, both the first on each transcript txNames(grl)