disengagementScore {ORFik} | R Documentation

## Disengagement score (DS)

### Description

Disengagement score is defined as

    (RPFs over ORF)/(RPFs downstream to tx end)

A pseudo-count of one is added to both the ORF and downstream sums.

### Usage

    disengagementScore(grl, RFP, GtfOrTx, RFP.sorted = FALSE)

### Arguments

`grl` | a `GRangesList` object with usually either leaders, cds', 3' utrs or ORFs.
`RFP` | RiboSeq reads as GAlignment, GRanges or GRangesList object
`GtfOrTx` | If it is `TxDb` object transcripts will be extracted using `exonsBy(Gtf, by = "tx", use.names = TRUE)`. Else it must be `GRangesList`
`RFP.sorted` | logical (F), an optimizer, have you ran this line: `RFP <- sort(RFP[countOverlaps(RFP, tx, type = "within") > 0])` Normally not touched, for internal optimization purposes.

### Value

a named vector of numeric values of scores

### References

doi: 10.1242/dev.098344

### See Also

Other features: `computeFeaturesCage`, `computeFeatures`, `distToCds`, `distToTSS`, `entropy`, `floss`, `fpkm_calc`, `fpkm`, `fractionLength`, `initiationScore`, `insideOutsideORF`, `isInFrame`, `isOverlapping`, `kozakSequenceScore`, `orfScore`, `rankOrder`, `ribosomeReleaseScore`, `ribosomeStallingScore`, `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)
    tx <- GRangesList(tx1 = GRanges("1", IRanges(1, 50), "+"))
    RFP <- GRanges("1", IRanges(c(1,10,20,30,40), width = 3), "+")
    disengagementScore(grl, RFP, tx)

[Package ORFik version 1.4.1 Index]