makeORFNames {ORFik} | R Documentation

## Make ORF names per orf

### Description

grl must be grouped by transcript If a list of orfs are grouped by transcripts, but does not have ORF names, then create them and return the new GRangesList

### Usage

    makeORFNames(grl, groupByTx = TRUE)

### Arguments

`grl` | a `GRangesList`
`groupByTx` | logical (T), should output GRangesList be grouped by transcripts (T) or by ORFs (F)?

### Value

(GRangesList) with ORF names, grouped by transcripts, sorted.

### 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 = gr_plus, tx2 = gr_minus)
    makeORFNames(grl)

[Package ORFik version 1.10.13 Index]