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, weight = 1L, overlapGrl = NULL)

### Arguments

`grl` | a `GRangesList` object with usually either leaders, cds', 3' utrs or ORFs.
`RFP` | RiboSeq reads as GAlignments, GRanges or GRangesList object
`weight` | a vector (default: 1L, if 1L it is identical to countOverlaps()), if single number (!= 1), it applies for all, if more than one must be equal size of 'reads'. else it must be the string name of a defined meta column in subject "reads", that gives number of times a read was found. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times.
`overlapGrl` | an integer, (default: NULL), if defined must be countOverlaps(grl, RFP), added for speed if you already have it

### 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()`, `countOverlapsW()`, `disengagementScore()`, `distToCds()`, `distToTSS()`, `entropy()`, `floss()`, `fpkm_calc()`, `fpkm()`, `fractionLength()`, `initiationScore()`, `insideOutsideORF()`, `isInFrame()`, `isOverlapping()`, `kozakSequenceScore()`, `orfScore()`, `rankOrder()`, `ribosomeReleaseScore()`, `startRegionCoverage()`, `startRegion()`, `stopRegion()`, `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 1.10.13 Index]