ribosomeReleaseScore: Ribosome Release Score (RRS)

In JokingHero/ORFik: Open Reading Frames in Genomics

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,
  weight.RFP = 1L,
  weight.RNA = 1L,
  overlapGrl = NULL
)

Arguments

grl	a GRangesList object with usually either leaders, cds', 3' utrs or ORFs.
RFP	RiboSeq reads as GAlignments, 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 GAlignments, GRanges or GRangesList object
weight.RFP	a vector (default: 1L). Can also be character name of column in RFP. As in translationalEff(weight = "score") for: GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times.
weight.RNA	Same as weightRFP but for RNA weights. (default: 1L)
overlapGrl	an integer, (default: NULL), if defined must be countOverlaps(grl, RFP), added for speed if you already have it

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: computeFeatures(), computeFeaturesCage(), countOverlapsW(), disengagementScore(), distToCds(), distToTSS(), entropy(), floss(), fpkm(), fpkm_calc(), fractionLength(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeStallingScore(), startRegion(), startRegionCoverage(), stopRegion(), 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)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.