## ----echo = FALSE------------------------------------------------------------- knitr::opts_chunk$set( eval=FALSE ) ## ----------------------------------------------------------------------------- # if(!"rWikiPathways" %in% installed.packages()){ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("rWikiPathways") # } # library(rWikiPathways) # # if(!"RCy3" %in% installed.packages()){ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("RCy3") # } # library(RCy3) # # # Use install.packages() for the following, if necessary: # library(magrittr) ## ----------------------------------------------------------------------------- # cytoscapePing() ## ----------------------------------------------------------------------------- # gbm.pathways <- findPathwaysByText('Glioblastoma') # many pathways returned # human.gbm.pathways <- gbm.pathways %>% # dplyr::filter(species == "Homo sapiens") # just the human gbm pathways ## ----------------------------------------------------------------------------- # human.gbm.wpids <- human.gbm.pathways$id ## ----------------------------------------------------------------------------- # commandsRun(paste0('wikipathways import-as-pathway id=',human.gbm.wpids[1])) ## ----------------------------------------------------------------------------- # openSession() # net.data <- getTableColumns(columns=c('name','degree.layout','COMMON')) # max.gene <- net.data[which.max(unlist(net.data['degree.layout'])),] # max.gene ## ----------------------------------------------------------------------------- # mcm1.pathways <-unique(findPathwayIdsByXref('YMR043W','En')) # commandsRun(paste0('wikipathways import-as-pathway id=', mcm1.pathways[1])) ## ----------------------------------------------------------------------------- # selectNodes('MCM1','name')