get_ensembl_ids {chimeraviz} | R Documentation |
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.
get_ensembl_ids(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 <- 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"