get_ensembl_ids {chimeraviz} | R Documentation

## Get ensembl ids for a fusion object

### Description

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

### Usage

    get_ensembl_ids(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 <- import_defuse(defuse833keFiltered, "hg19", 1)
    # Get a specific fusion
    fusion <- get_fusion_by_id(fusions, 5267)
    # See the ensembl ids:
    partner_gene_ensembl_id(upstream_partner_gene(fusion))
    # [1] "ENSG00000180198"
    partner_gene_ensembl_id(downstream_partner_gene(fusion))
    # [1] "ENSG00000162639"
    # Reset the fusion objects ensembl ids
    partner_gene_ensembl_id(upstream_partner_gene(fusion)) <- ""
    partner_gene_ensembl_id(downstream_partner_gene(fusion))  <- ""
    # Get the ensembl ids
    fusion <- get_ensembl_ids(fusion)
    # See that we now have the same ensembl ids again:
    partner_gene_ensembl_id(upstream_partner_gene(fusion))
    # [1] "ENSG00000180198"
    partner_gene_ensembl_id(downstream_partner_gene(fusion))
    # [1] "ENSG00000162639"

[Package chimeraviz version 1.6.2 Index]