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)

### Arguments

`grl` | a `GRangesList` object with usually either leaders, cds', 3' utrs or ORFs.
`RFP` | RiboSeq reads as GAlignment, GRanges or GRangesList object

### 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`, `entropy`, `floss`, `fpkm_calc`, `fpkm`, `fractionLength`, `insideOutsideORF`, `isInFrame`, `isOverlapping`, `kozakSequenceScore`, `orfScore`, `rankOrder`, `ribosomeReleaseScore`, `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 1.0.0 Index]