fractionLength {ORFik} | R Documentation

## Fraction Length

### Description

Fraction Length is defined as

    (lengths of grl)/(length of tx_len)

so that each group in the grl is divided by the corresponding transcript.

### Usage

    fractionLength(grl, tx_len)

### Arguments

`grl` | a `GRangesList` object with usually either leaders, cds', 3' utrs or ORFs. ORFs are a special case, see argument tx_len
`tx_len` | the transcript lengths of the transcripts, a named (tx names) vector of integers. If you have the transcripts as GRangesList, call 'ORFik:::widthPerGroup(tx, TRUE)'. If you used CageSeq to reannotate leaders, then the tss for the the leaders have changed, therefore the tx lengths have changed. To account for that call: 'tx_len <- widthPerGroup(extendLeaders(tx, cageFiveUTRs))' and calculate graction length using 'fractionLength(grl, tx_len)'.

### Value

a numeric vector of ratios

### References

doi: 10.1242/dev.098343

### See Also

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

### Examples

    ORF <- GRanges(seqnames = "1",
                   ranges = IRanges(start = c(1, 10, 20), end = c(5, 15, 25)),
                   strand = "+")
    grl <- GRangesList(tx1_1 = ORF)
    # grl must have same names as cds + _1 etc, so that they can be matched.
    tx <-  GRangesList(tx1 = GRanges("1", IRanges(1, 50), "+"))
    fractionLength(grl, ORFik:::widthPerGroup(tx, keep.names = TRUE))

[Package ORFik version 1.2.1 Index]