disengagementScore {ORFik}R Documentation

Disengagement score (DS)

Description

Disengagement score is defined as 

(RPFs over ORF)/(RPFs downstream to transcript 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 1.6.9 Index]