ribosomeReleaseScore {ORFik}R Documentation

Ribosome Release Score (RRS)

Description

Ribosome Release Score is defined as

(RPFs over ORF)/(RPFs over 3' utrs)

and additionaly normalized by lengths. If RNA is added as argument, it will normalize by RNA counts to justify location of 3' utrs. It can be understood as a ribosome stalling feature. A pseudo-count of one was added to both the ORF and downstream sums.

Usage

ribosomeReleaseScore(grl, RFP, GtfOrThreeUtrs, RNA = NULL)

Arguments

grl

a GRangesList object with usually either leaders, cds', 3' utrs or ORFs.

RFP

RiboSeq reads as GAlignment, GRanges or GRangesList object

GtfOrThreeUtrs

if Gtf: a TxDb object of a gtf file transcripts is called from: 'threeUTRsByTranscript(Gtf, use.names = TRUE)', if object is GRangesList, it is presumed to be the 3' utrs

RNA

RnaSeq reads as GAlignment, GRanges or GRangesList object

Value

a named vector of numeric values of scores, NA means that no 3' utr was found for that transcript.

References

doi: 10.1016/j.cell.2013.06.009

See Also

Other features: computeFeaturesCage, computeFeatures, disengagementScore, distToCds, distToTSS, entropy, floss, fpkm_calc, fpkm, fractionLength, initiationScore, insideOutsideORF, isInFrame, isOverlapping, kozakSequenceScore, orfScore, rankOrder, ribosomeStallingScore, startRegionCoverage, startRegion, subsetCoverage, translationalEff

Examples

ORF <- GRanges(seqnames = "1",
               ranges = IRanges(start = c(1, 10, 20), end = c(5, 15, 25)),
               strand = "+")
grl <- GRangesList(tx1_1 = ORF)
threeUTRs <- GRangesList(tx1 = GRanges("1", IRanges(40, 50), "+"))
RFP <- GRanges("1", IRanges(25, 25), "+")
RNA <- GRanges("1", IRanges(1, 50), "+")
ribosomeReleaseScore(grl, RFP, threeUTRs, RNA)


[Package ORFik version 1.4.0 Index]