## ---- echo = FALSE--------------------------------------------------------- knitr::opts_chunk$set( eval=FALSE ) ## -------------------------------------------------------------------------- # if(!"rWikiPathways" %in% installed.packages()){ # source("https://bioconductor.org/biocLite.R") # biocLite("rWikiPathways") # } # library(rWikiPathways) # if(!"BridgeDbR" %in% installed.packages()){ # source("https://bioconductor.org/biocLite.R") # biocLite("BridgeDbR") # } # library(BridgeDbR) ## -------------------------------------------------------------------------- # orgNames <- listOrganisms() # orgNames ## -------------------------------------------------------------------------- # unlist(lapply(orgNames,BridgeDbR::getOrganismCode)) ## -------------------------------------------------------------------------- # BridgeDbR::getSystemCode("Ensembl") ## -------------------------------------------------------------------------- # BridgeDbR::getSystemCode("Entrez Gene") ## -------------------------------------------------------------------------- # tnf.pathways <- findPathwayIdsByXref('TNF', getSystemCode('HGNC')) # tnf.pathways ## -------------------------------------------------------------------------- # getXrefList('WP554', getSystemCode('Ensembl')) ## -------------------------------------------------------------------------- # getXrefList('WP554', getSystemCode('ChEBI')) ## -------------------------------------------------------------------------- # BridgeDbR::getFullName('Ce')