txNames: Get transcript names from orf names

In JokingHero/ORFik: Open Reading Frames in Genomics

Get transcript names from orf names

Description

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

Usage

txNames(grl, ref = NULL, unique = FALSE)

Arguments

grl	a GRangesList grouped by ORF , GRanges object or IRanges object.
ref	a reference GRangesList. The object you want grl to subset by names. Add to make sure naming is valid.
unique	a boolean, if true unique the names, used if several orfs map to same transcript and you only want the unique groups

Details

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)

Value

a character vector of transcript names, without _* naming

See Also

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

Examples

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)

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