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)
grl |
a |
RFP |
RiboSeq reads as GAlignment, GRanges or GRangesList object |
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)