R: Add information on coding/non-coding status.

addIsCoding {refGenome} | R Documentation

## Add information on coding/non-coding status.

### Description

The `addIsCoding` method extracts positions from 'CDS' features in the `ensemblGenome` object. The positions of the 'CDS' features are compared with the splice-junction positions in the `ensemblJunctions` object. When a match is found, the splice junction is marked as coding, otherwise the junction is marked as non-coding. The coding information is calculated for each flanking exon of the splice-junction. The column name for the left side (lend) is `licd`, the name for the right side (rstart) is `ricd`.

### Usage

    addIsCoding(object,ens)

### Arguments

`object` | `ensemblJunctions`. The object to which `isCoding` columns are added.

`ens` | `ensemblGenome`. Genome object which should contain 'CDS' features.

### Author(s)

Wolfgang Kaisers

### Examples

    ef <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
    ens <- loadGenome(ef)
    enj <- getSpliceTable(ens)
    addIsCoding(enj, ens)

[Package refGenome version 1.7.7 Index]