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, weight = 1L, overlapGrl = NULL )
grl |
a |
RFP |
RiboSeq reads as GAlignments, GRanges or GRangesList object |
GtfOrTx |
If it is |
ds |
numeric vector (NULL), disengagement score. If you have already
calculated |
RFP.sorted |
logical (FALSE), an optimizer, have you ran this line:
|
weight |
a vector (default: 1L, if 1L it is identical to countOverlaps()), if single number (!= 1), it applies for all, if more than one must be equal size of 'reads'. else it must be the string name of a defined meta column in subject "reads", that gives number of times a read was found. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times. |
overlapGrl |
an integer, (default: NULL), if defined must be countOverlaps(grl, RFP), added for speed if you already have it |
a named vector of numeric values of scores
doi: 10.1242/dev.098345
Other features:
computeFeaturesCage()
,
computeFeatures()
,
countOverlapsW()
,
disengagementScore()
,
distToCds()
,
distToTSS()
,
entropy()
,
floss()
,
fpkm_calc()
,
fpkm()
,
fractionLength()
,
initiationScore()
,
isInFrame()
,
isOverlapping()
,
kozakSequenceScore()
,
orfScore()
,
rankOrder()
,
ribosomeReleaseScore()
,
ribosomeStallingScore()
,
startRegionCoverage()
,
startRegion()
,
stopRegion()
,
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)