ribosomeReleaseScore {ORFik} | R Documentation

## Ribosome Release Score (RRS)

### Description

Ribosome Release Score is defined as

    (RPFs over ORF)/(RPFs over 3' utrs)

and additionaly normalized by lengths. If RNA is added as argument, it will normalize by RNA counts to justify location of 3' utrs. It can be understood as a ribosome stalling feature. A pseudo-count of one was added to both the ORF and downstream sums.

### Usage

    ribosomeReleaseScore(
      grl,
      RFP,
      GtfOrThreeUtrs,
      RNA = NULL,
      weight.RFP = 1L,
      weight.RNA = 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
`GtfOrThreeUtrs` | if Gtf: a TxDb object of a gtf file transcripts is called from: 'threeUTRsByTranscript(Gtf, use.names = TRUE)', if object is GRangesList, it is presumed to be the 3' utrs
`RNA` | RnaSeq reads as `GAlignments`, `GRanges` or GRangesList object
`weight.RFP` | a vector (default: 1L). Can also be character name of column in RFP. As in translationalEff(weight = "score") for: GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times.
`weight.RNA` | Same as weightRFP but for RNA weights. (default: 1L)
`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 scores, NA means that no 3' utr was found for that transcript.

### References

doi: 10.1016/j.cell.2013.06.009

### See Also

Other features: `computeFeaturesCage()`, `computeFeatures()`, `countOverlapsW()`, `disengagementScore()`, `distToCds()`, `distToTSS()`, `entropy()`, `floss()`, `fpkm_calc()`, `fpkm()`, `fractionLength()`, `initiationScore()`, `insideOutsideORF()`, `isInFrame()`, `isOverlapping()`, `kozakSequenceScore()`, `orfScore()`, `rankOrder()`, `ribosomeStallingScore()`, `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)
    threeUTRs <- GRangesList(tx1 = GRanges("1", IRanges(40, 50), "+"))
    RFP <- GRanges("1", IRanges(25, 25), "+")
    RNA <- GRanges("1", IRanges(1, 50), "+")
    ribosomeReleaseScore(grl, RFP, threeUTRs, RNA)

[Package ORFik version 1.12.13 Index]