## ----echo = FALSE------------------------------------------------------------- knitr::opts_chunk$set( eval=FALSE ) ## ----------------------------------------------------------------------------- # if(!"rWikiPathways" %in% installed.packages()){ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("rWikiPathways") # } # library(rWikiPathways) # if(!"BridgeDbR" %in% installed.packages()){ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("BridgeDbR") # } # library(BridgeDbR) ## ----------------------------------------------------------------------------- # orgNames <- listOrganisms() # orgNames ## ----------------------------------------------------------------------------- # BridgeDbR::getOrganismCode(orgNames[1]) ## ----------------------------------------------------------------------------- # BridgeDbR::getSystemCode("Ensembl") ## ----------------------------------------------------------------------------- # BridgeDbR::getSystemCode("Entrez Gene") ## ----------------------------------------------------------------------------- # tnf.pathways <- findPathwayIdsByXref('TNF', BridgeDbR::getSystemCode('HGNC')) # tnf.pathways ## ----------------------------------------------------------------------------- # getXrefList('WP554', BridgeDbR::getSystemCode('Ensembl')) ## ----------------------------------------------------------------------------- # getXrefList('WP554', BridgeDbR::getSystemCode('ChEBI')) ## ----------------------------------------------------------------------------- # BridgeDbR::getFullName('Ce')