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]