ORF rank in transcripts

Description

ig. second orf _2 -> 2

Usage

rankOrder(grl)

Arguments

Value

a numeric vector of integers

References

doi: 10.1074/jbc.R116.733899

See Also

Other features: computeFeaturesCage, computeFeatures, disengagementScore, distToCds, entropy, floss, fpkm_calc, fpkm, fractionLength, insideOutsideORF, isInFrame, isOverlapping, kozakSequenceScore, orfScore, ribosomeReleaseScore, ribosomeStallingScore, subsetCoverage, translationalEff

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)
grl <- ORFik:::makeORFNames(grl)
rankOrder(grl)