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 1.4.0 Index]