defineTrailer: Defines trailers for ORF.

Description Usage Arguments Details Value See Also Examples

View source: R/ORFs_helpers.R

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

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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

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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)

ORFik documentation built on March 27, 2021, 6 p.m.