isInFrame {ORFik} | R Documentation

## Find frame for each orf relative to cds

### Description

Input of this function, is the output of the function [distToCds()], or any other relative ORF frame.

### Usage

    isInFrame(dists)

### Arguments

`dists` | a vector of integer distances between ORF and cds. 0 distance means equal frame

### Details

possible outputs: 0: orf is in frame with cds 1: 1 shifted from cds 2: 2 shifted from cds

### Value

a logical vector

### References

doi: 10.1074/jbc.R116.733899

### See Also

Other features: `computeFeaturesCage()`, `computeFeatures()`, `countOverlapsW()`, `disengagementScore()`, `distToCds()`, `distToTSS()`, `entropy()`, `floss()`, `fpkm_calc()`, `fpkm()`, `fractionLength()`, `initiationScore()`, `insideOutsideORF()`, `isOverlapping()`, `kozakSequenceScore()`, `orfScore()`, `rankOrder()`, `ribosomeReleaseScore()`, `ribosomeStallingScore()`, `startRegionCoverage()`, `startRegion()`, `stopRegion()`, `subsetCoverage()`, `translationalEff()`

### Examples

    # simple example
    isInFrame(c(3,6,8,11,15))

    # GRangesList example
    grl <- GRangesList(tx1_1 = GRanges("1", IRanges(1,10), "+"))
    fiveUTRs <- GRangesList(tx1 = GRanges("1", IRanges(1,20), "+"))
    dist <- distToCds(grl, fiveUTRs)
    isInFrame <- isInFrame(dist)

[Package ORFik version 1.12.13 Index]