## ----setup1, message= FALSE,results='hide',eval=FALSE---------------------- # #------------------------------------------------------------------------------- # # install.packages("BiocManager",repos = "http://cran.us.r-project.org") # BiocManager::install("gevaertlab/AMARETTO") # # #------------------------------------------------------------------------------- ## ----AMARETTO_Download1, message= FALSE,results='hide',eval=FALSE---------- # #------------------------------------------------------------------------------- # # library(AMARETTO) # TargetDirectory <- tempfile()# data download directory # CancerSite <- "LIHC" # DataSetDirectories <- AMARETTO_Download(CancerSite = CancerSite, # TargetDirectory = TargetDirectory) # # #------------------------------------------------------------------------------- ## ----AMARETTO_Preprocess, message= FALSE,results='hide',eval=FALSE--------- # #------------------------------------------------------------------------------- # # ProcessedData <- AMARETTO_Preprocess(DataSetDirectories = DataSetDirectories, # BatchData = BatchData) # # #------------------------------------------------------------------------------- ## ----ProcessedDataLIHC, message= FALSE,results='hide', echo=FALSE---------- library(AMARETTO) data(ProcessedDataLIHC) ## ----AMARETTO_Initialize, message= FALSE,results='hide'-------------------- #------------------------------------------------------------------------------- AMARETTOinit <- AMARETTO_Initialize(ProcessedData = ProcessedDataLIHC, NrModules = 2, VarPercentage = 50) #------------------------------------------------------------------------------- ## ----AMARETTO_Run, message= FALSE,warning=FALSE,results='hide'------------- #------------------------------------------------------------------------------- AMARETTOresults <- AMARETTO_Run(AMARETTOinit = AMARETTOinit) #------------------------------------------------------------------------------- ## ----AMARETTO_EvaluateTestSet, message= FALSE,results='hide'--------------- #------------------------------------------------------------------------------- AMARETTOtestReport <- AMARETTO_EvaluateTestSet( AMARETTOresults = AMARETTOresults, MA_Data_TestSet = AMARETTOinit$MA_matrix_Var, RegulatorData_TestSet = AMARETTOinit$RegulatorData ) #------------------------------------------------------------------------------- ## ----AMARETTO_VisualizeModule, message= FALSE, fig.height=5, fig.width=7, retina=1---- #------------------------------------------------------------------------------- ModuleNr <- 1 #define the module number to visualize AMARETTO_VisualizeModule(AMARETTOinit = AMARETTOinit, AMARETTOresults = AMARETTOresults, ProcessedData = ProcessedDataLIHC, ModuleNr = ModuleNr) #------------------------------------------------------------------------------- ## ----AMARETTO_HTMLreport, message= FALSE,results='hide', eval=FALSE,eval=FALSE---- # #------------------------------------------------------------------------------- # # gmt_file<-system.file("templates/H.C2CP.genesets.gmt",package="AMARETTO") # AMARETTO_HTMLreport(AMARETTOinit = AMARETTOinit,, # AMARETTOresults = AMARETTOresults, # ProcessedData = ProcessedDataLIHC, # hyper_geo_test_bool = TRUE, # hyper_geo_reference = gmt_file, # MSIGDB=TRUE) # # #------------------------------------------------------------------------------- ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()