orfScore {ORFik}R Documentation

Get ORFscore for a GRangesList of ORFs

Description

ORFscore tries to check whether the first frame of the 3 possible frames in an ORF has more reads than second and third frame.

Usage

orfScore(grl, RFP, is.sorted = FALSE)

Arguments

grl

a GRangesList object with ORFs

RFP

ribosomal footprints, given as Galignment object, Granges or GRangesList

is.sorted

logical (F), is grl sorted.

Details

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.

Value

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)

References

doi: 10.1002/embj.201488411

See Also

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

Examples

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)


[Package ORFik version 1.4.0 Index]