ribosomeStallingScore {ORFik}R Documentation

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, overlapGrl = countOverlaps(grl, RFP))

Arguments

grl

a GRangesList object with usually either leaders, cds', 3' utrs or ORFs.

RFP

RiboSeq reads as GAlignment, GRanges or GRangesList object

overlapGrl

an integer vector of overlaps (default: countOverlaps(grl, RFP))

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(), distToTSS(), entropy(), floss(), fpkm_calc(), fpkm(), fractionLength(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeReleaseScore(), 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)
RFP <- GRanges("1", IRanges(25, 25), "+")
ribosomeStallingScore(grl, RFP)


[Package ORFik version 1.6.9 Index]