distToTSS {ORFik} | R Documentation

## Get distances between ORF Start and TSS of its transcript

### Description

Matching is done by transcript names. This is applicable practically to the upstream (fiveUTRs) ORFs. If ORF is not within specified search space in fiveUTRs, this function will crash.

### Usage

    distToTSS(ORFs, fiveUTRs)

### Arguments

`ORFs` | orfs as `GRangesList`, names of orfs must be txname_[rank]
`fiveUTRs` | 5' leaders as `GRangesList`.

### Value

an integer vector, 1 means on TSS, 2 means second base of Tx.

### References

doi: 10.1074/jbc.R116.733899

### See Also

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

### Examples

    grl <- GRangesList(tx1_1 = GRanges("1", IRanges(5, 10), "+"))
    fiveUTRs <- GRangesList(tx1 = GRanges("1", IRanges(2, 20), "+"))
    distToTSS(grl, fiveUTRs)

[Package ORFik version 1.2.1 Index]