Ribosome Stalling Score (RSS)

Description

Is defined as

(RPFs over ORF stop sites)/(RPFs over ORFs)

and normalized by lengths A pseudo-count of one was added to both the ORF and downstream sums.

Usage

ribosomeStallingScore(grl, RFP)

Arguments

Value

a named vector of numeric values of RSS scores

References

doi: 10.1016/j.cels.2017.08.004

See Also

Other features: computeFeaturesCage, computeFeatures, disengagementScore, distToCds, entropy, floss, fpkm_calc, fpkm, fractionLength, insideOutsideORF, isInFrame, isOverlapping, kozakSequenceScore, orfScore, rankOrder, ribosomeReleaseScore, 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)
RFP <- GRanges("1", IRanges(25, 25), "+")
ribosomeStallingScore(grl, RFP)