ORF rank in transcripts

Description

Creates an ordering of ORFs per transcript, so that ORF with the most upstream start codon is 1, second most upstream start codon is 2, etc. Must input a grl made from ORFik, txNames_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(), countOverlapsW(), disengagementScore(), distToCds(), distToTSS(), entropy(), floss(), fpkm_calc(), fpkm(), fractionLength(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), ribosomeReleaseScore(), ribosomeStallingScore(), startRegionCoverage(), startRegion(), 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)