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]