| insideOutsideORF {ORFik} | R Documentation |
Inside/Outside score is defined as
(reads over ORF)/(reads outside ORF and within transcript)
A pseudo-count of one is added to both the ORF and outside sums.
insideOutsideORF(grl, RFP, GtfOrTx, ds = NULL, RFP.sorted = FALSE)
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 |
ds |
numeric vector (NULL), disengagement score. If you have already
calculated |
RFP.sorted |
logical (F), have you ran this line:
|
a named vector of numeric values of scores
doi: 10.1242/dev.098345
Other features:
computeFeaturesCage(),
computeFeatures(),
disengagementScore(),
distToCds(),
distToTSS(),
entropy(),
floss(),
fpkm_calc(),
fpkm(),
fractionLength(),
initiationScore(),
isInFrame(),
isOverlapping(),
kozakSequenceScore(),
orfScore(),
rankOrder(),
ribosomeReleaseScore(),
ribosomeStallingScore(),
startRegionCoverage(),
startRegion(),
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)