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 any region in Transcript If ORF is not within specified search space in tx, this function will crash.

### Usage

    distToTSS(ORFs, tx)

### Arguments

`ORFs` | orfs as `GRangesList`, names of orfs must be txname_[rank]
`tx` | transcripts 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()`, `countOverlapsW()`, `disengagementScore()`, `distToCds()`, `entropy()`, `floss()`, `fpkm_calc()`, `fpkm()`, `fractionLength()`, `initiationScore()`, `insideOutsideORF()`, `isInFrame()`, `isOverlapping()`, `kozakSequenceScore()`, `orfScore()`, `rankOrder()`, `ribosomeReleaseScore()`, `ribosomeStallingScore()`, `startRegionCoverage()`, `startRegion()`, `stopRegion()`, `subsetCoverage()`, `translationalEff()`

### Examples

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

[Package ORFik version 1.10.13 Index]