CSPC_MAE                A 'MultiAssayExperiment' containing cohorts of
                        pancreatic cancer patients, for use in package
                        examples.
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
ConsensusMetaclusteringModel
                        Constructor for a 'ConsensusClusterModel'
                        Object.
ConsensusMetaclusteringModel-class
                        An 'S4Model' Containing Molecular Data to be
                        Consensus Clustered
CoxModel                CoxModel constructor
GeneFuModel             'GeneFuModel' Constructor Method
GeneFuModel-class       A 'SurvivalModel' Sub-class Designed to Hold A
                        Survival Model Generated Using the 'genefu' R
                        package.
ModelComparison         ModelComparison Constructor
ModelComparison-class   ModelComparison Class Definition
NCSModel-class          S4Model Class for Metaclustering Using Network
                        Community Search
NetworkCommunitySearchModel
                        Constructor for a NetworkCommunitySearchModel
                        (NCSModel)
PCOSP                   Pancreatic Cancer Overall Survival Predictor
                        (PCOSP) Constructor
PCOSP-class             Pancreatic Cancer Overall Survival Predictor
                        (PCOSP) Class
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
RGAModel-class          RGAModel Class Definition
RLSModel-class          RLSModel Class Definition
RandomGeneAssignmentModel
                        RandomGeneAssignmentModel Constructor
RandomLabelShufflingModel
                        RandomLabelShufflingModel Constructor
S4Model-class           An 'S4' Virtual Class For the Concept of a
                        Statistical or ML Model
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
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
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.
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.
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
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
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
normalize,data.frame_or_matrix-method
                        Normalize a 'data.frame' 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.
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'.
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
runGSEA                 Run Gene Set Enrichment Analysis
runGSEA,PCOSP,data.frame-method
                        Run Gene Set Enrichment Analysis On A 'PCOSP'
                        Model Object.
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'
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'
