ribosomeStallingScore: Ribosome Stalling Score (RSS)

In Roleren/ORFik: Open Reading Frames in Genomics

Ribosome Stalling Score (RSS)

Description

Is defined as

(RPFs over ORF stop sites)/(RPFs over ORFs)

and normalized by lengths A pseudo-count of one was added to both the ORF and downstream sums.

Usage

ribosomeStallingScore(grl, RFP, weight = 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
weight	a numeric/integer vector or metacolumn name. (default: 1L, no differential weighting). If weight is name of defined meta column in reads object, it gives the number of times a read was found at that position. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times. if 1L it means each read is weighted equal as 1, this is what among others countOverlaps() presumes, if single number (!= 1), it repeats for all ranges, if vector with length > 1, it must be equal size of the reads object.
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 RSS scores

References

doi: 10.1016/j.cels.2017.08.004

See Also

Other features: computeFeatures(), computeFeaturesCage(), countOverlapsW(), disengagementScore(), distToCds(), distToTSS(), entropy(), floss(), fpkm(), fpkm_calc(), fractionLength(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeReleaseScore(), 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)
RFP <- GRanges("1", IRanges(25, 25), "+")
ribosomeStallingScore(grl, RFP)

Roleren/ORFik documentation built on Dec. 18, 2024, 11:39 p.m.