| insideOutsideORF {ORFik} | R Documentation |
Inside/Outside score is defined as
(reads over ORF)/(reads outside ORF and within transcript)
A pseudo-count of one was added to both the ORF and outside sums.
insideOutsideORF(grl, RFP, GtfOrTx)
grl |
a |
RFP |
ribo seq reads as GAlignment, GRanges or GRangesList object |
GtfOrTx |
if Gtf: a TxDb object of a gtf file that transcripts will be extracted with 'exonsBy(Gtf, by = "tx", use.names = TRUE)', if a GrangesList will use as is |
a named vector of numeric values of scores
doi: 10.1242/dev.098345
Other features: computeFeaturesCage,
computeFeatures,
disengagementScore,
distToCds, entropy,
floss, fpkm_calc,
fpkm, fractionLength,
isInFrame, isOverlapping,
kozakSequenceScore, orfScore,
rankOrder,
ribosomeReleaseScore,
ribosomeStallingScore,
subsetCoverage,
translationalEff
# Check inside outside score of a ORF within a transcript
ORF <- GRanges("1",
ranges = IRanges(start = c(20, 30, 40),
end = c(25, 35, 45)),
strand = "+")
grl <- GRangesList(tx1_1 = ORF)
tx1 <- GRanges(seqnames = "1",
ranges = IRanges(start = c(1, 10, 20, 30, 40, 50),
end = c(5, 15, 25, 35, 45, 200)),
strand = "+")
tx <- GRangesList(tx1 = tx1)
RFP <- GRanges(seqnames = "1",
ranges = IRanges(start = c(1, 4, 30, 60, 80, 90),
end = c(30, 33, 63, 90, 110, 120)),
strand = "+")
insideOutsideORF(grl, RFP, tx)