txNames {ORFik} | R Documentation

## 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)

[Package ORFik version 1.12.13 Index]