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, 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)