initiationScore: Get initiation score for a GRangesList of ORFs

In JokingHero/ORFik: Open Reading Frames in Genomics

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, reads, pShifted = TRUE, weight = "score")

Arguments

grl	a GRangesList object with ORFs
cds	a GRangesList object with coding sequences
tx	a GRangesList of transcripts covering grl.
reads	ribo seq reads as GAlignments, GRanges or GRangesList object
pShifted	a logical (TRUE), are riboseq reads p-shifted?
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.

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

If a score column is defined, it will use it as weights, see getWeights

Value

an integer vector, 1 score per ORF, with names of grl

References

doi: 10.1186/s12915-017-0416-0

See Also

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

Examples

# 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)

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