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 was added to both the ORF and outside sums.

### Usage

    insideOutsideORF(grl, RFP, GtfOrTx, ds = NULL, RFP.sorted = FALSE)

### Arguments

`grl` | a `GRangesList` object with usually either leaders, cds', 3' utrs or ORFs
`RFP` | ribo seq reads as GAlignment, GRanges or GRangesList object
`GtfOrTx` | if Gtf: a TxDb object of a gtf file that transcripts will be extracted with 'exonsBy(Gtf, by = "tx", use.names = TRUE)', if a GrangesList will use as is
`ds` | numeric vector (NULL), disengagement score. If you have already calculated `disengagementScore`, input here to save time.
`RFP.sorted` | logical (F), 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.098345

### See Also

Other features: `computeFeaturesCage`, `computeFeatures`, `disengagementScore`, `distToCds`, `distToTSS`, `entropy`, `floss`, `fpkm_calc`, `fpkm`, `fractionLength`, `initiationScore`, `isInFrame`, `isOverlapping`, `kozakSequenceScore`, `orfScore`, `rankOrder`, `ribosomeReleaseScore`, `ribosomeStallingScore`, `startRegionCoverage`, `startRegion`, `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 1.4.1 Index]