defineTrailer: Defines trailers for ORF.

In JokingHero/ORFik: Open Reading Frames in Genomics

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)

JokingHero/ORFik documentation built on Oct. 21, 2024, 11:42 a.m.