function Methylation() -> (CSV betaTable) {
    beta002raw = INPUT(path=dataDir+"/methylation/DNA_Methylation/JHU_USC__IlluminaDNAMethylation_OMA002_CPI/Level_2/jhu-usc.edu__IlluminaDNAMethylation_OMA002_CPI__beta-value")
    beta003raw= INPUT(path=dataDir+"/methylation/DNA_Methylation/JHU_USC__IlluminaDNAMethylation_OMA003_CPI/Level_2/jhu-usc.edu__IlluminaDNAMethylation_OMA003_CPI__beta-value")
    annotation002 = INPUT(path=dataDir+"/methylation/OMA-002-annotation.csv")
    annotation003 = INPUT(path=dataDir+"/methylation/OMA-003-annotation-geneids.csv")
    
    results002 = MethylationAnalysis(beta002raw, annotation002)
    results003 = MethylationAnalysis(beta003raw, annotation003)
    combined = CSVJoin(results002.beta, results003.beta, intersection=false)
    
    return combined.csv
}

function MethylationAnalysis(CSV betaRaw, CSV annotation) -> (CSV beta) {
    GENE_COMBINE_METHOD = "median"
    
    betaFilt1 = CSVFilter(force betaRaw,
        regexp="Hybridization REF=CompositeElement REF", includeColumns="", negate=true)
    betaFilt = SearchReplace(betaFilt1, key00="N/A", value00="NA")   
    groups = SampleGroupCreator(betaFilt.file, pattern1="(TCGA-[0-9]+-[0-9]+)-01.*", definition1="$1,median")
    beta = SampleCombiner(betaFilt, groups)
    betaNames = CSVTransformer(beta.expr,
        transform1="sapply(strsplit(csv1[,1], '_', fixed=TRUE), function(x) x[1])",
        transform2="csv1[,2:ncol(csv1)]", columnNames="c('GeneName', colnames(csv1)[2:ncol(csv1)])")
    betaUnique = IDConvert(betaNames.transformed,
        annotation,
        conversionColumn="GeneID",
        sourceColumn="GeneName",
        unique=true,
        collapseNumeric=GENE_COMBINE_METHOD)
    betaResults = CSVTransformer(betaUnique.csv,
        transform1="csv1[,1]",
        transform2="sapply(1:nrow(matrix1), function(i) median(matrix1[i,], na.rm=TRUE))",
        transform3="sapply(1:nrow(matrix1), function(i) sd(matrix1[i,], na.rm=TRUE))",
        columnNames="c('GeneID', 'Beta', 'BetaSD')")
    return betaResults.transformed
}