disengagementScore {ORFik} | R Documentation |
Disengagement score is defined as
(RPFs over ORF)/(RPFs downstream to transcript end)
A pseudo-count of one is added to both the ORF and downstream sums.
disengagementScore(grl, RFP, GtfOrTx, RFP.sorted = FALSE)
grl |
a |
RFP |
RiboSeq reads as GAlignment, GRanges or GRangesList object |
GtfOrTx |
If it is |
RFP.sorted |
logical (F), an optimizer, have you ran this line:
|
a named vector of numeric values of scores
doi: 10.1242/dev.098344
Other features:
computeFeaturesCage()
,
computeFeatures()
,
distToCds()
,
distToTSS()
,
entropy()
,
floss()
,
fpkm_calc()
,
fpkm()
,
fractionLength()
,
initiationScore()
,
insideOutsideORF()
,
isInFrame()
,
isOverlapping()
,
kozakSequenceScore()
,
orfScore()
,
rankOrder()
,
ribosomeReleaseScore()
,
ribosomeStallingScore()
,
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) tx <- GRangesList(tx1 = GRanges("1", IRanges(1, 50), "+")) RFP <- GRanges("1", IRanges(c(1,10,20,30,40), width = 3), "+") disengagementScore(grl, RFP, tx)