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##  AMARETTO: Regulatory network inference and driver gene evaluation using

##            integrative multi-omics analysis and penalized regression

##  For details on the implementation visit

##  https://github.com/gevaertlab/AMARETTO

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###################### Example R Script ##################

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# 1. Installing AMARETTO and loading the package:

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install.packages("BiocManager")

BiocManager::install("gevaertlab/AMARETTO")

library(AMARETTO)

resdir <- file.path("AMARETTO_Results");if(!file.exists(resdir))    dir.create(resdir) #Absolute path to data results directory

setwd(resdir)

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# 2. Dowloading TCGA input data for analysis

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TargetDirectory <- file.path(getwd(),"Downloads/");if(!file.exists(TargetDirectory))    dir.create(TargetDirectory) #Absolute path to data download directory

CancerSite <- "LIHC"

DataSetDirectories <- AMARETTO_Download(CancerSite,TargetDirectory = TargetDirectory)

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# 3. Preprocessing the downloaded TCGA data

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#ProcessedData <- AMARETTO_Preprocess(DataSetDirectories,BatchData)

#load(inst/extdata//MethylStates.rda) #MethylMix preprocessed data for CancerSite

#ProcessedData[[3]] <- MethylStates[CancerSite] #MethylMix preprocessed data for CancerSite

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# Loading preprocessed TCGA-LAML example dataset:

#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#

data("ProcessedDataLIHC")

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# 4. Running AMARETTO

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AMARETTOinit <- AMARETTO_Initialize(ProcessedDataLIHC,NrModules = 2, VarPercentage = 60)

AMARETTOresults <- AMARETTO_Run(AMARETTOinit)

AMARETTOtestReport <- AMARETTO_EvaluateTestSet(AMARETTOresults = AMARETTOresults,

                                               MA_Data_TestSet = AMARETTOinit$MA_matrix_Var,

                                               RegulatorData_TestSet = AMARETTOinit$RegulatorData)

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# 4. Visualize AMARETTO modules

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ModuleNr <- 1 #define the module number to visualize

AMARETTO_VisualizeModule(AMARETTOinit = AMARETTOinit,AMARETTOresults = AMARETTOresults,

                         ProcessedData = ProcessedDataLIHC,ModuleNr = ModuleNr)

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# 5. Get HTML report for AMARETTO modules

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AMARETTO_HTMLreport(AMARETTOinit,AMARETTOresults,ProcessedDataLIHC,VarPercentage=10,hyper_geo_test_bool=FALSE,output_address=resdir)