getEnsemblIds {chimeraviz} | R Documentation |
This function will get the ensembl ids from the org.Hs.eg.db package given the gene names of the fusion event.
getEnsemblIds(fusion)
fusion |
The Fusion object we want to get ensembl ids for. |
The Fusion object with Ensembl ids set.
# 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"