disengagementScore {ORFik} | R Documentation |
Disengagement score is defined as
(RPFs over ORF)/(RPFs downstream to tx 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)