doc/Joint_Pathway_Analysis.R

In simscr/metaboanalyst: An R Package for Comprehensive Analysis of Metabolomics Data

## ---- eval=FALSE---------------------------------------------------------
#  
#  download.file("https://www.metaboanalyst.ca/MetaboAnalyst/resources/data/integ_genes.txt", "integ_genes.txt", "curl")
#  
#  download.file("https://www.metaboanalyst.ca/MetaboAnalyst/resources/data/integ_cmpds.txt", "integ_cmpds.txt", "curl")
#  

## ---- eval=FALSE---------------------------------------------------------
#  library(MetaboAnalystR)
#  
#  # Initiate MetaboAnalyst
#  mSet<-InitDataObjects("conc", "pathinteg", FALSE)
#  
#  # Set organism library
#  mSet<-SetOrganism(mSet, "hsa")
#  
#  # Set the name of your file containing your gene list
#  geneListFile<-"integ_genes.txt"
#  
#  # Read in your gene list file
#  geneList<-readChar(geneListFile, file.info(geneListFile)$size)
#  
#  # Perform gene mapping of your file
#  mSet<-PerformIntegGeneMapping(mSet, geneList, "hsa", "symbol");
#  
#  # Set the name of your file containing your compound list
#  cmpdListFile<-"integ_cmpds.txt"
#  
#  # Read in your compound list file
#  cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
#  
#  # Perform compound mapping of your file
#  mSet<-PerformIntegCmpdMapping(mSet, cmpdList, "hsa", "kegg");
#  
#  # Create a mapping result table
#  mSet<-CreateMappingResultTable(mSet)
#  
#  # Prepare data for joint pathway analysis
#  mSet<-PrepareIntegData(mSet);
#  

## ---- eval=FALSE---------------------------------------------------------
#  #### OPTION 1 ####
#  # Perform integrated pathway analysis, using hypergeometric test, degree centrality, and the gene-metabolite pathways
#  # Saves the output as MetaboAnalyst_result_pathway.csv
#  mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ")
#  
#  # View the output of the pathway analysis
#  mSet$dataSet$path.mat
#  

## ---- eval=FALSE---------------------------------------------------------
#  #### OPTION 2 ####
#  # Perform integrated pathway analysis, using hypergeometric test, betweenness centrality, and gene-centric pathways
#  # Saves the output as MetaboAnalyst_result_pathway.csv
#  mSet<-PerformIntegPathwayAnalysis(mSet, "bc", "hyper", "genetic")
#  

## ---- eval=FALSE---------------------------------------------------------
#  # Perform pathway analysis
#  mSet<-PlotPathSummary(mSet, "path_view_0_", "png", 72, width=NA)