.ClinicalModel	ClinicalModel-class
.CohortList	CohortList-class
.ConsensusMetaclusteringModel	ConsensusMetaclusteringModel-class
.CoxModel	CoxModel-class
.findAllCohortPairs	dot-findAllCohortPairs
.GeneFuModel	GeneFuModel-class
.ModelComparison	ModelComparison-class
.NCSModel	NCSModel-class
.PCOSP	PCOSP-class
.randomSampleIndex	dot-randomSampleIndex
.RGAModel	RGAModel-class
.RLSModel	RLSModel-class
.S4Model	S4Model-class
.SurvivalExperiment	SurvivalExperiment-class
.SurvivalModel	SurvivalModel-class
assignColDataColumn	assignColDataColumn
assignSubtypes	assignSubtypes
assignSubtypes,CohortList,list-method	assignSubtypes-CohortList-list-method
assignSubtypes,SurvivalExperiment,data.frame-method	assignSubtypes-SurvivalExperiment-data.frame-method
barPlotModelComparison	barPlotModelComparison
barPlotModelComparison,ClinicalModel,PCOSP_or_RLS_or_RGA-method	barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method
birnbaum	birnbaum
chen	chen
ClinicalModel	ClinicalModel
ClinicalModel-class	ClinicalModel-class
CohortList	CohortList
CohortList-class	CohortList-class
cohortSubtypeDFs	cohortSubtypeDFs
compareModels	compareModels
compareModels,ModelComparison,SurvivalModel-method	compareModels-ModelComparison-SurvivalModel-method
compareModels,SurvivalModel,SurvivalModel-method	compareModels-SurvivalModel-SurvivalModel-method
ConMetaclustModel	ConsensusMetaclusteringModel
ConsensusMetaclusteringModel	ConsensusMetaclusteringModel
ConsensusMetaclusteringModel-class	ConsensusMetaclusteringModel-class
CoxModel	CoxModel
CoxModel-class	CoxModel-class
CSPC_MAE	CSPC_MAE
densityPlotModelComparison	densityPlotModelComparison
densityPlotModelComparison,PCOSP_or_RLS_or_RGA,PCOSP_or_RLS_or_RGA-method	densityPlotModelComparison-PCOSP_or_RLS_or_RGA-PCOSP_or_RLS_or_RGA-method
dropNotCensored	dropNotCensored
dropNotCensored,CohortList-method	dropNotCensored-CohortList-method
dropNotCensored,SurvivalExperiment-method	dropNotCensored-SurvivalExperiment-method
findCommonGenes	findCommonGenes
findCommonGenes,CohortList-method	findCommonGenes-CohortList-method
findCommonGenes,MultiAssayExperiment-method	findCommonGenes-MultiAssayExperiment-method
findCommonSamples	findCommonSamples
findCommonSamples,CohortList-method	findCommonSamples-CohortList-method
forestPlot	forestPlot
forestPlot,ModelComparison-method	forestPlot-ModelComparison-method
forestPlot,PCOSP_or_ClinicalModel-method	forestPlot-PCOSP_or_ClinicalModel-method
GeneFuModel	GeneFuModel
GeneFuModel-class	GeneFuModel-class
getModelSeed	getModelSeed
getModelSeed,SurvivalModel-method	getModelSeed-SurvivalModel-method
getTopFeatures	getTopFeatures
getTopFeatures,MultiAssayExperiment-method	getTopFeatures-MultiAssayExperiment-method
getTopFeatures,PCOSP-method	getTopFeatures-PCOSP-method
getTopFeatures,SummarizedExperiment-method	getTopFeatures-SummarizedExperiment-method
haiderSigScores	haiderSigScores
hasColDataColumns	hasColDataColumns
merge,SurvivalExperiment,SurvivalExperiment-method	merge-SurvivalExperiment-SurvivalExperiment-method
ModelComparison	ModelComparison
ModelComparison-class	ModelComparison-class
modelParams	modelParams
modelParams,S4Model-method	modelParams-S4Model-method
modelParams<-	modelParams-set
modelParams<-,S4Model,List_or_list_or_NULL-method	modelParams-set-S4Model-List_or_list_or_NULL-method
models	models
models,S4Model-method	models-S4Model-method
models,SurvivalModel-method	models-SurvivalModel-method
models<-	models-set
models<-,S4Model,List_or_list_or_NULL-method	models-set-S4Model-List_or_list_or_NULL-method
models<-,SurvivalModel,SimpleList-method	models-set-SurvivalModel-SimpleList-method
NCSModel	NetworkCommunitySearchModel
NCSModel-class	NCSModel-class
NetworkCommunitySearchModel	NetworkCommunitySearchModel
normalize,data.frame_or_matrix-method	normalize-data.frame_or_matrix-method
normalize,DFrame-method	normalize-DFrame-method
normalize,MultiAssayExperiment-method	normalize-MultiAssayExperiment-method
normalize,SummarizedExperiment-method	normalize-SummarizedExperiment-method
normalsMAE	normalsMAE
PCOSP	PCOSP
PCOSP-class	PCOSP-class
PCOSP_or_ClinicalModel-class	PCOSP_or_ClinicalModel-class
PCOSP_or_RLS_or_RGA-class	PCOSP_or_RLS_or_RGA-class
plotNetworkGraph	plotNetworkGraph
plotNetworkGraph,NCSModel-method	plotNetworkGraph-NCSModel-method
plotROC	plotROC
plotROC,PCOSP-method	plotROC-PCOSP-method
plotSurvivalCurves	plotSurvivalCurves
plotSurvivalCurves,CoxModel-method	plotSurvivalCurves-CoxModel-method
predictClasses	predictClasses
predictClasses,CohortList,ClinicalModel-method	predictClasses-CohortList-ClinicalModel-method
predictClasses,CohortList,GeneFuModel-method	predictClasses-CohortList-GeneFuModel-method
predictClasses,CohortList,PCOSP_or_RLS_or_RGA-method	predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method
predictClasses,ConsensusMetaclusteringModel,ANY-method	predictClasses-ConsensusMetaclusteringModel-ANY-method
predictClasses,NCSModel,ANY-method	predictClasses-NCSModel-ANY-method
predictClasses,SurvivalExperiment,ClinicalModel-method	predictClasses-SurvivalExperiment-ClinicalModel-method
predictClasses,SurvivalExperiment,GeneFuModel-method	predictClasses-SurvivalExperiment-GeneFuModel-method
predictClasses,SurvivalExperiment,PCOSP_or_RLS_or_RGA-method	predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method
preprocessCaret	preprocessCaret
RandomGeneAssignmentModel	RandomGeneAssignmentModel
RandomLabelShufflingModel	RandomLabelShufflingModel
rankFeatures	rankFeatures
rankFeatures,MultiAssayExperiment-method	rankFeatures-MultiAssayExperiment-method
rankFeatures,SummarizedExperiment-method	rankFeatures-SummarizedExperiment-method
removeColDataFactorColumns	removeColDataFactorColumns
removeFactorColumns	removeFactorColumns
renameColDataColumns	renameColDataColumns
renameColumns	renameColumns
RGAModel	RandomGeneAssignmentModel
RGAModel-class	RGAModel-class
RLSModel	RandomLabelShufflingModel
RLSModel-class	RLSModel-class
runGSEA	runGSEA
runGSEA,PCOSP,data.frame-method	runGSEA-PCOSP-data.frame-method
S4Model-class	S4Model-class
sampleClinicalModel	sampleClinicalModel
sampleCohortList	sampleCohortList
sampleICGCmicro	sampleICGCmicro
samplePCOSPmodel	samplePCOSPmodel
samplePCOSPpredList	samplePCOSPpredList
samplePCSIsurvExp	samplePCSIsurvExp
sampleRGAmodel	sampleRGAmodel
sampleRLSmodel	sampleRLSmodel
sampleTrainedPCOSPmodel	sampleTrainedPCOSPmodel
sampleValPCOSPmodel	sampleValPCOSPmodel
show,S4Model-method	show-S4Model-method
subset,CohortList-method	subset-CohortList-method
SurvivalExperiment	SurvivalExperiment
SurvivalExperiment-class	SurvivalExperiment-class
SurvivalModel	SurvivalModel
SurvivalModel-class	SurvivalModel-class
trainData	trainData
trainData,S4Model-method	trainData-S4Model-method
trainData<-	trainData-set
trainData<-,S4Model-method	trainData-set-S4Model-method
trainModel	trainModel
trainModel,ClinicalModel-method	trainModel-ClinicalModel-method
trainModel,ConsensusMetaclusteringModel-method	trainModel-ConsensusMetaclusteringModel-method
trainModel,CoxModel-method	trainModel-CoxModel-method
trainModel,GeneFuModel-method	trainModel-GeneFuModel-method
trainModel,NCSModel-method	trainModel-NCSModel-method
trainModel,PCOSP-method	trainModel-PCOSP-method
trainModel,RGAModel-method	trainModel-RGAModel-method
trainModel,RLSModel-method	trainModel-RLSModel-method
validateModel	validateModel
validateModel,ClinicalModel,CohortList-method	validateModel-ClinicalModel-CohortList-method
validateModel,ClinicalModel,SurvivalExperiment-method	validateModel-ClinicalModel-SurvivalExperiment-method
validateModel,ConsensusMetaclusteringModel,ConsensusMetaclusteringModel-method	validateModel-ConsensusMetaclusteringModel-ConsensusMetaclusteringModel-method
validateModel,GeneFuModel,CohortList-method	validateModel-GeneFuModel-CohortList-method
validateModel,GeneFuModel,SurvivalExperiment-method	validateModel-GeneFuModel-SurvivalExperiment-method
validateModel,PCOSP_or_RLS_or_RGA,CohortList-method	validateModel-PCOSP_or_RLS_or_RGA-CohortList-method
validateModel,PCOSP_or_RLS_or_RGA,SurvivalExperiment-method	validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method
validationData	validationData
validationData,S4Model-method	validationData-S4Model-method
validationData,SurvivalModel-method	validationData-SurvivalModel-method
validationData<-	validationData-set
validationData<-,S4Model,List_or_list_or_NULL-method	validationData-set-S4Model-List_or_list_or_NULL-method
validationData<-,SurvivalModel,CohortList-method	validationData-set-SurvivalModel-CohortList-method
validationStats	validationStats
validationStats,S4Model-method	validationStats-S4Model-method
validationStats,SurvivalModel-method	validationStats-SurvivalModel-method
validationStats<-	validationStats-set
validationStats<-,S4Model,DFrame_or_data.frame_data.table_or_NULL-method	validationStats-set-S4Model-DFrame_or_data.frame_data.table_or_NULL-method
validationStats<-,SurvivalModel,data.frame-method	validationStats-set-SurvivalModel-data.frame-method
