insideOutsideORF: Inside/Outside score (IO)

In JokingHero/ORFik: Open Reading Frames in Genomics

Inside/Outside score (IO)

Description

Inside/Outside score is defined as

(reads over ORF)/(reads outside ORF and within transcript)

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

Usage

insideOutsideORF(
  grl,
  RFP,
  GtfOrTx,
  ds = NULL,
  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
ds	numeric vector (NULL), disengagement score. If you have already calculated disengagementScore, input here to save time.
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.098345

See Also

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

Examples

# Check inside outside score of a ORF within a transcript
ORF <- GRanges("1",
               ranges = IRanges(start = c(20, 30, 40),
                                  end = c(25, 35, 45)),
               strand = "+")

grl <- GRangesList(tx1_1 = ORF)

tx1 <- GRanges(seqnames = "1",
               ranges = IRanges(start = c(1, 10, 20, 30, 40, 50),
                                end = c(5, 15, 25, 35, 45, 200)),
               strand = "+")
tx <- GRangesList(tx1 = tx1)
RFP <- GRanges(seqnames = "1",
                  ranges = IRanges(start = c(1, 4, 30, 60, 80, 90),
                                   end = c(30, 33, 63, 90, 110, 120)),
                  strand = "+")

insideOutsideORF(grl, RFP, tx)

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