assignColDataColumn     assignColDataColumn Assign a new column
                        directly to the colData slot of a
                        SummarizedExperiment.
assignSubtypes          Assign Sample Subtypes to an S4 Object
assignSubtypes,CohortList,list-method
                        Assign Subtype Annotations to a
                        SurvivalExperiment Object
assignSubtypes,SurvivalExperiment,data.frame-method
                        Assign Subtype Annotations to a
                        SurvivalExperiment Object
barPlotModelComparison
                        Make A Bar Plot Comparing Performance Between
                        Two 'S4' Objects Representing Mathematical
                        Models.
barPlotModelComparison,ClinicalModel,PCOSP_or_RLS_or_RGA-method
                        Make a Bar Plot Comparison Model Performance
                        Between a ClinicalModel and a PCOSP, RLSModel
                        or RGAModel object.
birnbaum                Published classifier gene signature for
                        Birnbaum
chen                    Published classifier gene signature for Chen
ClinicalModel           Constructor for the ClinicalModel Class
ClinicalModel-class     ClinicalModel Class Definition
CohortList              Constructor for the CohortList class, a
                        specialized list for storing SurvivalExperiment
                        objects.
CohortList-class        CohortList Class Definition
cohortSubtypeDFs        A list of sample subtypes for the data in
                        sampleCohortList
compareModels           Compare Two Mathematical Models Represented as
                        'S4' Objects
compareModels,ModelComparison,SurvivalModel-method
                        Compare Two 'SurivalModel' Objects, Returing A
                        'ModelComparison' Object With Statistics
                        Comparing the Performance of Each Model.
compareModels,SurvivalModel,SurvivalModel-method
                        Compare Two 'SurivalModel' Objects, Returing A
                        'ModelComparison' Object With Statistics
                        Comparing the Performance of Each Model.
ConsensusMetaclusteringModel
                        Constructor for a 'ConsensusClusterModel'
                        Object.
ConsensusMetaclusteringModel-class
                        An 'S4Model' Containing Molecular Data to be
                        Consensus Clustered
CoxModel                CoxModel constructor
CSPC_MAE                A 'MultiAssayExperiment' containing cohorts of
                        pancreatic cancer patients, for use in package
                        examples.
densityPlotModelComparison
                        Render A Density Plot of Model Performance for
                        an 'S4' Object
densityPlotModelComparison,PCOSP_or_RLS_or_RGA,PCOSP_or_RLS_or_RGA-method
                        Render a Density Plot Comparing Model
                        Performance Between Two 'PCOSP', 'RLSModel' or
                        'RGAModel' object.
dropNotCensored         Remove Censored Patient Samples from An 'S4'
                        Object.
dropNotCensored,CohortList-method
                        Remove Censored Patients from Each
                        'SurvivalExperiemnt' in a 'CohortList'
dropNotCensored,SurvivalExperiment-method
                        Remove Censored Patients from A
                        'SurvivalExperiment' Object
existingClassifierData
                        existingClassifierData
findCommonGenes         Find the common genes in an 'S4' object.
findCommonGenes,CohortList-method
                        Intersect Gene Names for All
                        'SurvivalExperiments' in a 'CohortList'
findCommonGenes,MultiAssayExperiment-method
                        Intersect Gene Names for All 'experiments' in a
                        'MultiAssayExperiment'
findCommonSamples       Find Common Samples in a List-like S4 Object
                        where The Columns of Each Item Represent
                        Samples
findCommonSamples,CohortList-method
                        Find Common Samples in a CohortList Object
                        where The Columns of Each Item Represent
                        Samples
forestPlot              Generate a forest plot from an 'S4' object
forestPlot,ModelComparison-method
                        Render a forest plot from the 'validationStats'
                        slot of a 'PCOSP' model object.
forestPlot,PCOSP_or_ClinicalModel-method
                        Render a forest plot from the 'validationStats'
                        slot of a 'PCOSP' model object.
GeneFuModel             'GeneFuModel' Constructor Method
GeneFuModel-class       A 'SurvivalModel' Sub-class Designed to Hold A
                        Survival Model Generated Using the 'genefu' R
                        package.
getModelSeed            Generic for retrieving the randomSeed parameter
                        from a 'SurvivalModel' object.
getModelSeed,SurvivalModel-method
                        Method for retrieving the random seed used for
                        training a specific survival model object.
getTopFeatures          Get the Top Predictive Features from an S4
                        Object
getTopFeatures,MultiAssayExperiment-method
                        Get the Top Ranked Features in a
                        'MultiAssayExperiment' object
getTopFeatures,PCOSP-method
                        Get the top features for classification using a
                        PCOSP model object.
getTopFeatures,SummarizedExperiment-method
                        Get the Top Ranked Features in a
                        'SummarizedExperiment' object
haiderSigScores         Classifier survival scores for Haider
hasColDataColumns       Check for Column Names in the colData Slot of a
                        SummarizedExperiment
merge,SurvivalExperiment,SurvivalExperiment-method
                        Merge two 'SurvivalExperiments', subsetting to
                        shared rows and columns
ModelComparison         ModelComparison Constructor
ModelComparison-class   ModelComparison Class Definition
modelParams             Generic for Accessing the Model Parameters of
                        an 'S4' Object
modelParams,S4Model-method
                        Accessor for the Model Parameters of an
                        'S4Model' Object
models                  Accessor for the models slot of an 'S4' object
models,S4Model-method   Getter for the models slot of an 'S4Model'
                        Object
models,SurvivalModel-method
                        Getter for the models slot of a 'SurvivalModel'
                        object
models<-,SurvivalModel,SimpleList-method
                        Setter for the models slot of a 'SurvivalModel'
                        object
NCSModel-class          S4Model Class for Metaclustering Using Network
                        Community Search
NetworkCommunitySearchModel
                        Constructor for a NetworkCommunitySearchModel
                        (NCSModel)
normalize,data.frame_or_matrix-method
                        Normalize a 'data.frame' Object
normalize,DFrame-method
                        Normalize a S4 'DFrame' Object
normalize,MultiAssayExperiment-method
                        Normalize the 'assays' of a
                        'MutliAssayExperiment' Object
normalize,SummarizedExperiment-method
                        Normalize the 'assays' in a
                        'SummarizedExperiment' Object
normalsMAE              A 'MultiAssayExperiment' containing cohorts of
                        normal patients, for package examples.
optimalKMinimizeAmbiguity
                        Predict optimal K values by minimizing the
                        difference between the ECDF of clustering
                        consensus at two points in a subinterval.
PCOSP                   Pancreatic Cancer Overall Survival Predictor
                        (PCOSP) Constructor
PCOSP_or_ClinicalModel-class
                        Class Union for PCOSP and ClinicalModel Types
PCOSP_or_RLS_or_RGA-class
                        Class Union for PCOSP, RLSModel and RGAModel
                        Types
PCOSP-class             Pancreatic Cancer Overall Survival Predictor
                        (PCOSP) Class
plotNetworkGraph        A Generic for Plotting a Network Graph From an
                        S4 Object
plotNetworkGraph,NCSModel-method
                        Plot a Network Graph for a Classified NCSModel
                        Object
plotROC                 Plot ROC curves for an 'S4' object
plotROC,PCOSP-method    Plot ROC curves for a 'PCOSP' model object.
plotSurvivalCurves      Generic for Plotting Survival Curves from an
                        'S4' Object
plotSurvivalCurves,CoxModel-method
                        Plot Survival Curves from a Fit 'CoxModel'
                        Object
predictClasses          Predict Classes for New Data Based on a Train
                        Classifier Model
predictClasses,CohortList,ClinicalModel-method
                        Use a Clinical GLM to Predict Classes for a
                        'CohortList' of 'SurvivalExperment' Objects.
predictClasses,CohortList,GeneFuModel-method
                        Use a Gene Signature Based Prediciton Model
                        from the 'genefu' Package to Predict Signature
                        Scores for Each Sample
predictClasses,CohortList,PCOSP_or_RLS_or_RGA-method
                        Predict Survival Prognosis Classes and Risk
                        Scores for A 'CohortList' Using a 'PCOSP',
                        'RLSModel' or 'RGAModel' object.
predictClasses,ConsensusMetaclusteringModel,ANY-method
                        Compute the Optimal Clustering Solution for a
                        Trained ConsensusMetaclusteringModel
predictClasses,NCSModel,ANY-method
                        Predict Metacluster Labels for a
                        NetworkCommunitySearchModel
predictClasses,SurvivalExperiment,ClinicalModel-method
                        Predict Survival Prognosis Classes and Risk
                        Scores for A 'SurvivalModel' Using a
                        'ClinicalModel' Object.
predictClasses,SurvivalExperiment,GeneFuModel-method
                        Use a Gene Signature Based Prediciton Model
                        from the 'genefu' Package to Predict Signature
                        Scores for Each Sample.
predictClasses,SurvivalExperiment,PCOSP_or_RLS_or_RGA-method
                        Predict Survival Prognosis Classes and Risk
                        Scores for A 'CohortList' Using a 'PCOSP',
                        'RLSModel' or 'RGAModel' object.
preprocessCaret         Preprocess Data Using the 'caret::preProcess'
                        method, then return the normalized data using
                        'predict'.
RandomGeneAssignmentModel
                        RandomGeneAssignmentModel Constructor
RandomLabelShufflingModel
                        RandomLabelShufflingModel Constructor
rankFeatures            Rank the Features in a 'S4' Object
rankFeatures,MultiAssayExperiment-method
                        Rank the Features in a 'MultiAssayExperiment'
                        Object
rankFeatures,SummarizedExperiment-method
                        Rank the Features in a 'SummarizedExperiment'
                        Object
removeColDataFactorColumns
                        Remave any factor columns from the 'colData' of
                        an 'S4' object
removeFactorColumns     Convert factor columns in a rectangular object
renameColDataColumns    Rename the columns in the 'colData' slot, or do
                        nothing if they don't match
renameColumns           Rename columns or do nothing if the names don't
                        match
RGAModel-class          RGAModel Class Definition
RLSModel-class          RLSModel Class Definition
runGSEA                 Run Gene Set Enrichment Analysis
runGSEA,PCOSP,data.frame-method
                        Run Gene Set Enrichment Analysis On A 'PCOSP'
                        Model Object.
S4Model-class           An 'S4' Virtual Class For the Concept of a
                        Statistical or ML Model
sampleClinicalModel     Sample ClinicalModel Containing the ICGC
                        micro-array cohort from 'MetaGxPancreas' as
                        training data.
sampleCohortList        A Set of Example Patient Cohorts
sampleICGCmicro         A Sample SurvivalExperiment Containing Data
                        from the ICGC micro-array cohort from
                        'MetaGxPancreas'
samplePCOSPmodel        A Sample PCOSP Model Containing the ICGC
                        micro-array cohort from 'MetaGxPancreas' as
                        training data.
samplePCOSPpredList     Sample CohortList with PCOSP Risk Predictions
samplePCSIsurvExp       Sample SurvivalExperiment Containing the PCSI
                        rna-sequencing cohort from 'MetaGxPancreas'.
sampleRGAmodel          Sample RGA Model Containing the ICGC
                        micro-array cohort from 'MetaGxPancreas' as
                        training data.
sampleRLSmodel          Sample RLS Model Containing the ICGC
                        micro-array cohort from 'MetaGxPancreas' as
                        training data.
sampleTrainedPCOSPmodel
                        A Sample Trained PCOSP Model Containing the
                        ICGC micro-array cohort from 'MetaGxPancreas'
                        as training data.
sampleValPCOSPmodel     Sample Validated PCOSP Model for Plotting
                        Examples
show,S4Model-method     Show method for Classes Inheriting from
                        'S4Model'
subset,CohortList-method
                        Subset method for a 'CohortList'
SurvivalExperiment      Constructor for 'SurvivalExperiment' Class
                        Builds a 'SurvivalExperiment' object, which is
                        just a wrapper for a 'SummarizedExperiment'
                        with mandatory survival metadata numeric
                        columns 'survival_time' and 'event_occurred'.
SurvivalExperiment-class
                        SurvivalExperiment Class
SurvivalModel           Constructor for a SurvivalModel Object.
SurvivalModel-class     A Generic Container for Storing Mathematical
                        Models of SurvivalExperiments
trainData               Generic for Accessing the Training Data of an
                        'S4' Object
trainData,S4Model-method
                        Accessor for the Training Data in a 'S4Model'
                        Object
trainData<-             Generic for Accessing the Training Data of an
                        'S4' Object
trainModel              Train a Model Based on the Data in an S4 Object
trainModel,ClinicalModel-method
                        Fit a GLM Using Clinical Predictors Specified
                        in a 'ClinicalModel' Object.
trainModel,ConsensusMetaclusteringModel-method
                        Train A ConsensusMetaclusteringModel
trainModel,CoxModel-method
                        Fit Models to the trainData in a CoxModel
                        Object
trainModel,GeneFuModel-method
                        Train a GeneFuModel Object
trainModel,NCSModel-method
                        Train a NetworkCommunitySearchModel
trainModel,PCOSP-method
                        Train a PCOSP Model Based on The Data the assay
                        'trainMatrix'.
trainModel,RGAModel-method
                        Train a RGAModel Based on the Data in the
                        assays slot.
trainModel,RLSModel-method
                        Train a PCOSP Model Based on The Data the assay
                        'trainMatrix'.
validateModel           Perform Validation on an 'S4' Object
                        Representing a Trained Model
validateModel,ClinicalModel,CohortList-method
                        Evaluate the Performance of a List of Trained
                        KTSP Models from a PCOSP Model
validateModel,ClinicalModel,SurvivalExperiment-method
                        Validate a ClinicalModel object with a single
                        SurvivalExperiment object.
validateModel,ConsensusMetaclusteringModel,ConsensusMetaclusteringModel-method
                        Compute the Inter-Cohort Cluster Correlation
                        and Clustering Reproducibility of All Clusters
                        in Each Cohort.
validateModel,GeneFuModel,CohortList-method
                        Evaluate the Performance of a List of Trained
                        KTSP Models from a PCOSP Model
validateModel,GeneFuModel,SurvivalExperiment-method
                        Validate a 'GenefuModel' object with a single
                        'SurvivalExperiment' object.
validateModel,PCOSP_or_RLS_or_RGA,CohortList-method
                        Evaluate the Performance of a List of Trained
                        KTSP Models from a PCOSP Model
validateModel,PCOSP_or_RLS_or_RGA,SurvivalExperiment-method
                        Validate a PCOSP model with a single
                        SurvivalExperiment object.
validationData          Accessor for the 'validationData' slot of an
                        'S4' object
validationData,S4Model-method
                        Accessor for the 'validationData' slot of an
                        'S4Model' object
validationData,SurvivalModel-method
                        Accessor for the 'validationData' slot of a
                        'SurvivalModel' object.
validationData<-        Generic for setting the 'validationData' slot
                        on an 'S4' object
validationData<-,SurvivalModel,CohortList-method
                        Setter for the 'validationData' slot of a
                        'SurvivalModel' object with a 'CohortList'.
validationStats         Accessor for the 'validationStats' slot of an
                        'S4' object
validationStats,S4Model-method
                        Acessor for the 'validationStats' slot of an
                        'S4Model' Object
validationStats,SurvivalModel-method
                        Accessor for the 'validationStats' slot of a
                        'SurvivalModel' object.
validationStats<-       Setter for the 'validationStats' slot on an
                        'S4' object
validationStats<-,S4Model,DFrame_or_data.frame_data.table_or_NULL-method
                        Setter for the 'validationStats' slot on an
                        'S4Model' object
validationStats<-,SurvivalModel,data.frame-method
                        Setter for the validationStats slot of a
                        'SurvivalModel' object with a 'data.frame'
