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, 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 vector (default: 1L, if 1L it is identical to countOverlaps()), if single number (!= 1), it applies for all, if more than one must be equal size of 'reads'. else it must be the string name of a defined meta column in subject "reads", that gives number of times a read was found. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times.

### 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: `computeFeaturesCage()`, `computeFeatures()`, `countOverlapsW()`, `disengagementScore()`, `distToCds()`, `distToTSS()`, `entropy()`, `floss()`, `fpkm_calc()`, `fpkm()`, `fractionLength()`, `insideOutsideORF()`, `isInFrame()`, `isOverlapping()`, `kozakSequenceScore()`, `orfScore()`, `rankOrder()`, `ribosomeReleaseScore()`, `ribosomeStallingScore()`, `startRegionCoverage()`, `startRegion()`, `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)

[Package ORFik version 1.14.7 Index]