disengagementScore: Disengagement score (DS)

In JokingHero/ORFik: Open Reading Frames in Genomics

Disengagement score (DS)

Description

Disengagement score is defined as

(RPFs over ORF)/(RPFs downstream to transcript end)

A pseudo-count of one is added to both the ORF and downstream sums.

Usage

disengagementScore(
  grl,
  RFP,
  GtfOrTx,
  RFP.sorted = FALSE,
  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
GtfOrTx	If it is TxDb object transcripts will be extracted using exonsBy(Gtf, by = "tx", use.names = TRUE). Else it must be GRangesList
RFP.sorted	logical (FALSE), an optimizer, have you ran this line: RFP <- sort(RFP[countOverlaps(RFP, tx, type = "within") > 0]) Normally not touched, for internal optimization purposes.
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 scores

References

doi: 10.1242/dev.098344

See Also

Other features: computeFeatures(), computeFeaturesCage(), countOverlapsW(), distToCds(), distToTSS(), entropy(), floss(), fpkm(), fpkm_calc(), fractionLength(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeReleaseScore(), 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)
tx <- GRangesList(tx1 = GRanges("1", IRanges(1, 50), "+"))
RFP <- GRanges("1", IRanges(c(1,10,20,30,40), width = 3), "+")
disengagementScore(grl, RFP, tx)

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