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)