insideOutsideORF {ORFik} | R Documentation

## Inside/Outside score (IO)

### Description

Inside/Outside score is defined as

    (reads over ORF)/(reads outside ORF and within transcript)

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

### Usage

    insideOutsideORF(
      grl,
      RFP,
      GtfOrTx,
      ds = NULL,
      RFP.sorted = FALSE,
      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
`GtfOrTx` | If it is `TxDb` object transcripts will be extracted using `exonsBy(Gtf, by = "tx", use.names = TRUE)`. Else it must be `GRangesList`
`ds` | numeric vector (NULL), disengagement score. If you have already calculated `disengagementScore`, input here to save time.
`RFP.sorted` | logical (FALSE), an optimizer, have you ran this line: `RFP <- sort(RFP[countOverlaps(RFP, tx, type = "within") > 0])` Normally not touched, for internal optimization purposes.
`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 scores

### References

doi: 10.1242/dev.098345

### See Also

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

### Examples

    # Check inside outside score of a ORF within a transcript
    ORF <- GRanges("1",
                   ranges = IRanges(start = c(20, 30, 40),
                                      end = c(25, 35, 45)),
                   strand = "+")

    grl <- GRangesList(tx1_1 = ORF)

    tx1 <- GRanges(seqnames = "1",
                   ranges = IRanges(start = c(1, 10, 20, 30, 40, 50),
                                    end = c(5, 15, 25, 35, 45, 200)),
                   strand = "+")
    tx <- GRangesList(tx1 = tx1)
    RFP <- GRanges(seqnames = "1",
                      ranges = IRanges(start = c(1, 4, 30, 60, 80, 90),
                                       end = c(30, 33, 63, 90, 110, 120)),
                      strand = "+")

    insideOutsideORF(grl, RFP, tx)

[Package ORFik version 1.12.13 Index]