stopCodons {ORFik} | R Documentation

## Get the Stop codons (3 bases) from a GRangesList of orfs grouped by orfs

### Description

In ATGTTTTGA, get the positions TGA. It takes care of exons boundaries, with exons < 3 length.

### Usage

    stopCodons(grl, is.sorted = FALSE)

### Arguments

`grl` | a `GRangesList` object
`is.sorted` | a boolean, a speedup if you know the ranges are sorted

### Value

a GRangesList of stop codons, since they might be split on exons

### See Also

Other ORFHelpers: `defineTrailer`, `longestORFs`, `mapToGRanges`, `orfID`, `startCodons`, `startSites`, `stopSites`, `txNames`, `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 = gr_plus, tx2 = gr_minus)
    stopCodons(grl, is.sorted = FALSE)

[Package ORFik version 1.4.1 Index]