getEnsemblIds {chimeraviz} | R Documentation

## Get ensembl ids for a fusion object

### Description

This function will get the ensembl ids from the org.Hs.eg.db package given the gene names of the fusion event.

### Usage

    getEnsemblIds(fusion)

### Arguments

`fusion` | The Fusion object we want to get ensembl ids for.

### Value

The Fusion object with Ensembl ids set.

### Examples

    # Import the filtered defuse results
    defuse833keFiltered <- system.file(
      "extdata",
      "defuse_833ke_results.filtered.tsv",
      package="chimeraviz")
    fusions <- importDefuse(defuse833keFiltered, "hg19", 1)
    # Get a specific fusion
    fusion <- getFusionById(fusions, 5267)
    # See the ensembl ids:
    partnerGeneEnsemblId(upstreamPartnerGene(fusion))
    # [1] "ENSG00000180198"
    partnerGeneEnsemblId(downstreamPartnerGene(fusion))
    # [1] "ENSG00000162639"
    # Reset the fusion objects ensembl ids
    partnerGeneEnsemblId(upstreamPartnerGene(fusion)) <- ""
    partnerGeneEnsemblId(downstreamPartnerGene(fusion))  <- ""
    # Get the ensembl ids
    fusion <- getEnsemblIds(fusion)
    # See that we now have the same ensembl ids again:
    partnerGeneEnsemblId(upstreamPartnerGene(fusion))
    # [1] "ENSG00000180198"
    partnerGeneEnsemblId(downstreamPartnerGene(fusion))
    # [1] "ENSG00000162639"

[Package chimeraviz version 1.4.3 Index]