| initiationScore {ORFik} | R Documentation |
initiationScore tries to check how much each TIS region resembles, the average of the CDS TIS regions.
initiationScore(grl, cds, tx, reads, pShifted = TRUE)
grl |
a |
cds |
a |
tx |
a GrangesList of transcripts covering grl. |
reads |
ribosomal footprints, given as Galignment object or Granges |
pShifted |
a logical (TRUE), are riboseq reads p-shifted? |
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
an integer vector, 1 score per ORF, with names of grl
doi: 10.1186/s12915-017-0416-0
Other features: computeFeaturesCage,
computeFeatures,
disengagementScore,
distToCds, distToTSS,
entropy, floss,
fpkm_calc, fpkm,
fractionLength,
insideOutsideORF, isInFrame,
isOverlapping,
kozakSequenceScore, orfScore,
rankOrder,
ribosomeReleaseScore,
ribosomeStallingScore,
startRegionCoverage,
startRegion, subsetCoverage,
translationalEff
# Good hiting ORF
ORF <- GRanges(seqnames = "1",
ranges = IRanges(21, 40),
strand = "+")
names(ORF) <- c("tx1")
grl <- GRangesList(tx1 = ORF)
# 1 width p-shifted reads
reads <- GRanges("1", IRanges(c(21, 23, 50, 50, 50, 53, 53, 56, 59),
width = 1), "+")
score(reads) <- 28 # original width
cds <- GRanges(seqnames = "1",
ranges = IRanges(50, 80),
strand = "+")
cds <- GRangesList(tx1 = cds)
tx <- GRanges(seqnames = "1",
ranges = IRanges(1, 85),
strand = "+")
tx <- GRangesList(tx1 = tx)
initiationScore(grl, cds, tx, reads, pShifted = TRUE)