| ribosomeStallingScore {ORFik} | R Documentation |
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.
ribosomeStallingScore(grl, RFP, overlapGrl = countOverlaps(grl, RFP))
grl |
a |
RFP |
RiboSeq reads as GAlignment, GRanges or GRangesList object |
overlapGrl |
an integer vector of overlaps (default: countOverlaps(grl, RFP)) |
a named vector of numeric values of RSS scores
doi: 10.1016/j.cels.2017.08.004
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()
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)