defineTrailer {ORFik} | R Documentation

## Defines trailers for ORF.

### Description

Creates GRanges object as a trailer for ORFranges representing ORF, maintaining restrictions of transcriptRanges. Assumes that ORFranges is on the transcriptRanges, strands and seqlevels are in agreement. When lengthOFtrailer is smaller than space left on the transcript than all available space is returned as trailer.

### Usage

    defineTrailer(ORFranges, transcriptRanges, lengthOftrailer = 200)

### Arguments

`ORFranges` | GRanges object of your Open Reading Frame.
`transcriptRanges` | GRanges object of transtript.
`lengthOftrailer` | Numeric. Default is 10.

### Details

It assumes that ORFranges and transcriptRanges are not sorted when on minus strand. Should be like: (200, 600) (50, 100)

### Value

A GRanges object of trailer.

### See Also

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

### Examples

    ORFranges <- GRanges(seqnames = Rle(rep("1", 3)),
                         ranges = IRanges(start = c(1, 10, 20),
                                          end = c(5, 15, 25)),
                         strand = "+")
    transcriptRanges <- GRanges(seqnames = Rle(rep("1", 5)),
                                ranges = IRanges(start = c(1, 10, 20, 30, 40),
                                                 end = c(5, 15, 25, 35, 45)),
                         strand = "+")
    defineTrailer(ORFranges, transcriptRanges)

[Package ORFik version 1.8.6 Index]