floss {ORFik} | R Documentation

## Fragment Length Organization Similarity Score

### Description

This feature is usually calcualted only for RiboSeq reads. For reads of width between 'start' and 'end', sum the fraction of RiboSeq reads (per widths) that overlap ORFs and normalize by CDS.

### Usage

    floss(grl, RFP, cds, start = 26, end = 34)

### Arguments

`grl` | a `GRangesList` object with ORFs
`RFP` | ribosomal footprints, given as Galignment or GRanges object, must be already shifted and resized to the p-site
`cds` | a `GRangesList` of coding sequences, cds has to have names as grl so that they can be matched
`start` | usually 26, the start of the floss interval
`end` | usually 34, the end of the floss interval

### Details

Pseudo explanation of the function:

    SUM[start to stop]((grl[start:end][name]/grl) / (cds[start:end][name]/cds))

Please read more in the article.

### Value

a vector of FLOSS of length same as grl

### References

doi: 10.1016/j.celrep.2014.07.045

### See Also

Other features: `computeFeaturesCage`, `computeFeatures`, `disengagementScore`, `distToCds`, `entropy`, `fpkm_calc`, `fpkm`, `fractionLength`, `insideOutsideORF`, `isInFrame`, `isOverlapping`, `kozakSequenceScore`, `orfScore`, `rankOrder`, `ribosomeReleaseScore`, `ribosomeStallingScore`, `subsetCoverage`, `translationalEff`

### Examples

    ORF <- GRanges(seqnames = "1",
                   ranges = IRanges(start = c(1, 12, 22),
                   end = c(10, 20, 32)),
                   strand = "+")
    grl <- GRangesList(tx1_1 = ORF)
    # RFP is 1 width position based GRanges
    RFP <- GRanges("1", IRanges(c(1, 25, 35, 38), width = 1), "+")
    score(RFP) <- c(28, 28, 28, 29) # original width in score col
    cds <-  GRangesList(tx1 = GRanges("1", IRanges(35, 44), "+"))
    # grl must have same names as cds + _1 etc, so that they can be matched.
    floss(grl, RFP, cds)
    # or change ribosome start/stop, more strict
    floss(grl, RFP, cds, 28, 28)

[Package ORFik version 1.0.0 Index]