orfScore {ORFik} | R Documentation |
ORFscore tries to check whether the first frame of the 3 possible frames in an ORF has more reads than second and third frame.
orfScore(grl, RFP, is.sorted = FALSE)
grl |
a |
RFP |
ribosomal footprints, given as Galignment object, Granges or GRangesList |
is.sorted |
logical (F), is grl sorted. |
Pseudocode: assume rff - is reads fraction in specific frame
ORFScore = log(rrf1 + rrf2 + rrf3)
For all ORFs where rrf2 or rrf3 is bigger than rff1, negate the resulting value.
ORFScore[rrf1Smaller] <- ORFScore[rrf1Smaller] * -1
As result there is one value per ORF: Positive values say that the first frame have the most reads, negative values say that the first frame does not have the most reads. NOTE: If reads are not of size 1, then a read from 1-4 on range of 1-4, will get scores frame1 = 2, frame2 = 1, frame3 = 1. What could be logical is that only the 5' end is important, so that only frame1 = 1, to get this, you first resize reads to 5'end only.
a data.table with 4 columns, the orfscore (ORFScores) and score of each of the 3 tiles (frame_zero_RP, frame_one_RP, frame_two_RP)
doi: 10.1002/embj.201488411
Other features: computeFeaturesCage
,
computeFeatures
,
disengagementScore
,
distToCds
, distToTSS
,
entropy
, floss
,
fpkm_calc
, fpkm
,
fractionLength
,
initiationScore
,
insideOutsideORF
, isInFrame
,
isOverlapping
,
kozakSequenceScore
,
rankOrder
,
ribosomeReleaseScore
,
ribosomeStallingScore
,
startRegionCoverage
,
startRegion
, subsetCoverage
,
translationalEff
ORF <- GRanges(seqnames = "1", ranges = IRanges(start = c(1, 10, 20), end = c(5, 15, 25)), strand = "+") names(ORF) <- c("tx1", "tx1", "tx1") grl <- GRangesList(tx1_1 = ORF) RFP <- GRanges("1", IRanges(25, 25), "+") # 1 width position based score(RFP) <- 28 # original width orfScore(grl, RFP) # negative because more hits on frames 1,2 than 0. # example with positive result, more hits on frame 0 (in frame of ORF) RFP <- GRanges("1", IRanges(c(1, 1, 1, 25), width = 1), "+") score(RFP) <- c(28, 29, 31, 28) # original width orfScore(grl, RFP)