## ---- echo = FALSE--------------------------------------------------------- knitr::opts_chunk$set( eval=FALSE ) ## -------------------------------------------------------------------------- # if(!"rWikiPathways" %in% installed.packages()){ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("rWikiPathways") # } # library(rWikiPathways) # if(!"RCy3" %in% installed.packages()){ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("RCy3") # } # library(RCy3) ## -------------------------------------------------------------------------- # cytoscapePing() ## -------------------------------------------------------------------------- # gbm.pathways <- findPathwaysByText('Glioblastoma') # many pathways returned # human.filter <- lapply(gbm.pathways, function(x) x$species == "Homo sapiens") # human.gbm.pathways <- gbm.pathways[unlist(human.filter)] # just the human BRCA2 pathways ## -------------------------------------------------------------------------- # human.gbm.wpids <- unique(unlist(lapply(human.gbm.pathways, function(x) x$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')