rankOrder {ORFik} | R Documentation

## 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

`grl` | a `GRangesList` object with ORFs

### Value

a numeric vector of integers

### References

doi: 10.1074/jbc.R116.733899

### See Also

Other features: `computeFeaturesCage`, `computeFeatures`, `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)

[Package ORFik version 1.4.1 Index]