disengagementScore: Disengagement score (DS)

In ORFik: Open Reading Frames in Genomics

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 vector (default: 1L, if 1L it is identical to countOverlaps()), if single number (!= 1), it applies for all, if more than one must be equal size of 'reads'. else it must be the string name of a defined meta column in subject "reads", that gives number of times a read was found. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times.
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: computeFeaturesCage(), computeFeatures(), countOverlapsW(), distToCds(), distToTSS(), entropy(), floss(), fpkm_calc(), fpkm(), fractionLength(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeReleaseScore(), ribosomeStallingScore(), startRegionCoverage(), startRegion(), 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)

ORFik documentation built on March 27, 2021, 6 p.m.