initiationScore {ORFik}R Documentation

Get initiation score for a GRangesList of ORFs

Description

initiationScore tries to check how much each TIS region resembles, the average of the CDS TIS regions.

Usage

initiationScore(grl, cds, tx, footprints, pShifted = TRUE)

Arguments

grl

a GRangesList object with ORFs

cds

a GRangesList object with coding sequences

tx

a GrangesList of transcripts covering grl.

footprints

ribosomal footprints, given as Galignment object or Granges

pShifted

a logical (TRUE), are riboseq reads p-shifted?

Details

Since this features uses a distance matrix for scoring, values are distributed like this: As result there is one value per ORF: 0.000: means that ORF had no reads -1.000: means that ORF is identical to average of CDS 1.000: means that orf is maximum different than average of CDS

Value

an integer vector, 1 score per ORF

References

doi: 10.1186/s12915-017-0416-0

See Also

Other features: computeFeaturesCage, computeFeatures, disengagementScore, distToCds, distToTSS, entropy, floss, fpkm_calc, fpkm, fractionLength, insideOutsideORF, isInFrame, isOverlapping, kozakSequenceScore, orfScore, rankOrder, ribosomeReleaseScore, ribosomeStallingScore, subsetCoverage, translationalEff

Examples

# Good hiting ORF
ORF <- GRanges(seqnames = "1",
               ranges = IRanges(start = c(21), end = c(40)),
               strand = "+")
names(ORF) <- c("tx1")
grl <- GRangesList(tx1 = ORF)
# 1 width position based
RFP <- GRanges("1", IRanges(c(21, 23, 50, 50, 50, 53, 53, 56, 59),
 c(21, 23, 50, 50, 50, 53, 53, 56, 59)), "+")
score(RFP) <- 28 # original width
cds <- GRanges(seqnames = "1",
               ranges = IRanges(start = c(50), end = c(80)),
               strand = "+")
cds <- GRangesList(tx1 = cds)
tx <- GRanges(seqnames = "1",
               ranges = IRanges(1,85),
               strand = "+")
tx <- GRangesList(tx1 = tx)

initiationScore(grl, cds, tx, RFP, pShifted = TRUE)


[Package ORFik version 1.2.1 Index]