# Generated by roxygen2: do not edit by hand

export("modelParams<-")
export("models<-")
export("trainData<-")
export("validationData<-")
export("validationStats<-")
export()
export(.plotNetwork)
export(ClinicalModel)
export(CohortList)
export(ConMetaclustModel)
export(ConsensusMetaclusteringModel)
export(CoxModel)
export(GeneFuModel)
export(ModelComparison)
export(NCSModel)
export(NetworkCommunitySearchModel)
export(PCOSP)
export(RGAModel)
export(RLSModel)
export(RandomGeneAssignmentModel)
export(RandomLabelShufflingModel)
export(SurvivalExperiment)
export(SurvivalModel)
export(assignColDataColumn)
export(assignSubtypes)
export(barPlotModelComparison)
export(compareModels)
export(densityPlotModelComparison)
export(dropNotCensored)
export(findCommonGenes)
export(findCommonSamples)
export(forestPlot)
export(getModelSeed)
export(getTopFeatures)
export(hasColDataColumns)
export(modelParams)
export(models)
export(optimalKMinimizeAmbiguity)
export(plotNetworkGraph)
export(plotROC)
export(plotSurvivalCurves)
export(predictClasses)
export(preprocessCaret)
export(rankFeatures)
export(removeColDataFactorColumns)
export(removeFactorColumns)
export(renameColDataColumns)
export(renameColumns)
export(runGSEA)
export(trainData)
export(trainModel)
export(validateModel)
export(validationData)
export(validationStats)
exportClasses(ClinicalModel)
exportClasses(CohortList)
exportClasses(ConsensusMetaclusteringModel)
exportClasses(CoxModel)
exportClasses(GeneFuModel)
exportClasses(ModelComparison)
exportClasses(NCSModel)
exportClasses(PCOSP)
exportClasses(RGAModel)
exportClasses(RLSModel)
exportClasses(S4Model)
exportClasses(SurvivalExperiment)
exportClasses(SurvivalModel)
exportMethods("modelParams<-")
exportMethods("models<-")
exportMethods("trainData<-")
exportMethods("validationData<-")
exportMethods("validationStats<-")
exportMethods(assignSubtypes)
exportMethods(barPlotModelComparison)
exportMethods(compareModels)
exportMethods(densityPlotModelComparison)
exportMethods(dropNotCensored)
exportMethods(findCommonGenes)
exportMethods(findCommonSamples)
exportMethods(forestPlot)
exportMethods(getModelSeed)
exportMethods(getTopFeatures)
exportMethods(merge)
exportMethods(modelParams)
exportMethods(models)
exportMethods(normalize)
exportMethods(plotNetworkGraph)
exportMethods(plotROC)
exportMethods(plotSurvivalCurves)
exportMethods(predictClasses)
exportMethods(rankFeatures)
exportMethods(runGSEA)
exportMethods(show)
exportMethods(subset)
exportMethods(trainData)
exportMethods(trainModel)
exportMethods(validateModel)
exportMethods(validationData)
exportMethods(validationStats)
import(BiocGenerics)
import(S4Vectors)
import(reportROC)
import(survcomp)
import(survival)
import(verification)
importClassesFrom(MultiAssayExperiment,MultiAssayExperiment)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,SimpleList)
importClassesFrom(data.table,data.table)
importFrom(BiocGenerics,mad)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(ConsensusClusterPlus,ConsensusClusterPlus)
importFrom(CoreGx,.collapse)
importFrom(CoreGx,.errorMsg)
importFrom(CoreGx,.warnMsg)
importFrom(MatrixGenerics,rowMads)
importFrom(MultiAssayExperiment,"experiments<-")
importFrom(MultiAssayExperiment,ExperimentList)
importFrom(MultiAssayExperiment,experiments)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,mendoapply)
importFrom(S4Vectors,merge)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,na.omit)
importFrom(S4Vectors,rename)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(caret,confusionMatrix)
importFrom(caret,preProcess)
importFrom(clusterRepro,clusterRepro)
importFrom(data.table,.N)
importFrom(data.table,.SD)
importFrom(data.table,`:=`)
importFrom(data.table,as.data.table)
importFrom(data.table,copy)
importFrom(data.table,data.table)
importFrom(data.table,fifelse)
importFrom(data.table,is.data.table)
importFrom(data.table,melt.data.table)
importFrom(data.table,merge.data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,set)
importFrom(data.table,setDF)
importFrom(data.table,setcolorder)
importFrom(data.table,setnames)
importFrom(data.table,transpose)
importFrom(data.table,tstrsplit)
importFrom(dplyr,dense_rank)
importFrom(genefu,sig.score)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_pointrange)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_step)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guides)
importFrom(ggplot2,labeller)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_x_reverse)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,vars)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggplotify,as.ggplot)
importFrom(ggplotify,base2grob)
importFrom(igraph,as.undirected)
importFrom(igraph,fastgreedy.community)
importFrom(igraph,graph_from_edgelist)
importFrom(igraph,layout_with_dh)
importFrom(igraph,layout_with_fr)
importFrom(igraph,membership)
importFrom(igraph,plot.igraph)
importFrom(matrixStats,weightedMedian)
importFrom(methods,is)
importFrom(pROC,coords)
importFrom(pROC,roc)
importFrom(piano,loadGSC)
importFrom(piano,runGSAhyper)
importFrom(plyr,is.formula)
importFrom(reportROC,reportROC)
importFrom(rlang,trace_back)
importFrom(scales,scientific)
importFrom(stats,as.formula)
importFrom(stats,binomial)
importFrom(stats,cor.test)
importFrom(stats,ecdf)
importFrom(stats,glm)
importFrom(stats,pchisq)
importFrom(stats,pnorm)
importFrom(stats,predict)
importFrom(stats,qnorm)
importFrom(stats,reformulate)
importFrom(stats,reorder)
importFrom(survival,Surv)
importFrom(survival,coxph)
importFrom(survival,strata)
importFrom(survival,survdiff)
importFrom(survival,survfit)
importFrom(survminer,ggsurvplot)
importFrom(survminer,ggsurvplot_facet)
importFrom(switchBox,SWAP.KTSP.Classify)
importFrom(switchBox,SWAP.KTSP.Train)
importFrom(utils,capture.output)
importFrom(utils,packageName)
importFrom(verification,roc.area)
importMethodsFrom(BiocGenerics,normalize)
importMethodsFrom(S4Vectors,subset)
