ribosomeStallingScore {ORFik} | R Documentation

## Ribosome Stalling Score (RSS)

### Description

Is defined as

    (RPFs over ORF stop sites)/(RPFs over ORFs)

and normalized by lengths A pseudo-count of one was added to both the ORF and downstream sums.

### Usage

    ribosomeStallingScore(grl, RFP, overlapGrl = countOverlaps(grl, RFP))

### Arguments

`grl` | a `GRangesList` object with usually either leaders, cds', 3' utrs or ORFs.
`RFP` | RiboSeq reads as GAlignment, GRanges or GRangesList object
`overlapGrl` | an integer vector of overlaps (default: countOverlaps(grl, RFP))

### Value

a named vector of numeric values of RSS scores

### References

doi: 10.1016/j.cels.2017.08.004

### See Also

Other features: `computeFeaturesCage()`, `computeFeatures()`, `disengagementScore()`, `distToCds()`, `distToTSS()`, `entropy()`, `floss()`, `fpkm_calc()`, `fpkm()`, `fractionLength()`, `initiationScore()`, `insideOutsideORF()`, `isInFrame()`, `isOverlapping()`, `kozakSequenceScore()`, `orfScore()`, `rankOrder()`, `ribosomeReleaseScore()`, `startRegionCoverage()`, `startRegion()`, `subsetCoverage()`, `translationalEff()`

### Examples

    ORF <- GRanges(seqnames = "1",
                   ranges = IRanges(start = c(1, 10, 20), end = c(5, 15, 25)),
                   strand = "+")
    grl <- GRangesList(tx1_1 = ORF)
    RFP <- GRanges("1", IRanges(25, 25), "+")
    ribosomeStallingScore(grl, RFP)

[Package ORFik version 1.6.9 Index]