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)