Man pages for bhklab/PDATK
Pancreatic Ductal Adenocarcinoma Tool-Kit
| assignColDataColumn | assignColDataColumn Assign a new column directly to the... |
| 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'... |
| barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method | Make a Bar Plot Comparison Model Performance Between a... |
| 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... |
| 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... |
| compareModels-SurvivalModel-SurvivalModel-method | Compare Two 'SurivalModel' Objects, Returing A... |
| ConsensusMetaclusteringModel | Constructor for a 'ConsensusClusterModel' Object. |
| ConsensusMetaclusteringModel-class | An 'S4Model' Containing Molecular Data to be Consensus... |
| CoxModel | CoxModel constructor |
| CoxModel-class | CoxModel-class |
| CSPC_MAE | A 'MultiAssayExperiment' containing cohorts of pancreatic... |
| 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... |
| dot-findAllCohortPairs | Find all non-self pair-wise combinations of cohorts |
| dot-randomSampleIndex | Generate a random sample from each group |
| dropNotCensored | Remove Censored Patient Samples from An 'S4' Object. |
| dropNotCensored-CohortList-method | Remove Censored Patients from Each 'SurvivalExperiemnt' in a... |
| 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... |
| findCommonGenes-MultiAssayExperiment-method | Intersect Gene Names for All 'experiments' in a... |
| findCommonSamples | Find Common Samples in a List-like S4 Object where The... |
| findCommonSamples-CohortList-method | Find Common Samples in a CohortList Object where The Columns... |
| forestPlot | Generate a forest plot from an 'S4' object |
| forestPlot-ModelComparison-method | Render a forest plot from the 'validationStats' slot of a... |
| forestPlot-PCOSP_or_ClinicalModel-method | Render a forest plot from the 'validationStats' slot of a... |
| GeneFuModel | 'GeneFuModel' Constructor Method |
| GeneFuModel-class | A 'SurvivalModel' Sub-class Designed to Hold A Survival Model... |
| getModelSeed | Generic for retrieving the randomSeed parameter from a... |
| getModelSeed-SurvivalModel-method | Method for retrieving the random seed used for training a... |
| getTopFeatures | Get the Top Predictive Features from an S4 Object |
| getTopFeatures-MultiAssayExperiment-method | Get the Top Ranked Features in a 'MultiAssayExperiment'... |
| getTopFeatures-PCOSP-method | Get the top features for classification using a PCOSP model... |
| getTopFeatures-SummarizedExperiment-method | Get the Top Ranked Features in a 'SummarizedExperiment'... |
| haiderSigScores | Classifier survival scores for Haider |
| hasColDataColumns | Check for Column Names in the colData Slot of a... |
| merge-SurvivalExperiment-SurvivalExperiment-method | Merge two 'SurvivalExperiments', subsetting to shared rows... |
| 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 |
| modelParams-set | Generic for Setting the Model Parameters of An 'S4' Object |
| modelParams-set-S4Model-List_or_list_or_NULL-method | Setter for the 'modelParams' of an 'S4Model' |
| models | Accessor for the models slot of an 'S4' object |
| models-S4Model-method | Getter for the models slot of an 'S4Model' Object |
| models-set | Accessor for the models slot of an 'S4' object |
| models-set-S4Model-List_or_list_or_NULL-method | Setter for the Models Slot of an 'S4Model' Object |
| models-set-SurvivalModel-SimpleList-method | Setter for the models slot of a 'SurvivalModel' object |
| models-SurvivalModel-method | Getter for the models slot of a 'SurvivalModel' object |
| NCSModel-class | S4Model Class for Metaclustering Using Network Community... |
| 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... |
| optimalKMinimizeAmbiguity | Predict optimal K values by minimizing the difference between... |
| PCOSP | Pancreatic Cancer Overall Survival Predictor (PCOSP)... |
| 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 |
| 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... |
| predictClasses-CohortList-ClinicalModel-method | Use a Clinical GLM to Predict Classes for a 'CohortList' of... |
| predictClasses-CohortList-GeneFuModel-method | Use a Gene Signature Based Prediciton Model from the 'genefu'... |
| predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method | Predict Survival Prognosis Classes and Risk Scores for A... |
| predictClasses-ConsensusMetaclusteringModel-ANY-method | Compute the Optimal Clustering Solution for a Trained... |
| predictClasses-NCSModel-ANY-method | Predict Metacluster Labels for a NetworkCommunitySearchModel |
| predictClasses-SurvivalExperiment-ClinicalModel-method | Predict Survival Prognosis Classes and Risk Scores for A... |
| predictClasses-SurvivalExperiment-GeneFuModel-method | Use a Gene Signature Based Prediciton Model from the 'genefu'... |
| predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method | Predict Survival Prognosis Classes and Risk Scores for A... |
| preprocessCaret | Preprocess Data Using the 'caret::preProcess' method, then... |
| 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'... |
| removeFactorColumns | Convert factor columns in a rectangular object |
| renameColDataColumns | Rename the columns in the 'colData' slot, or do nothing if... |
| 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... |
| sampleClinicalModel | Sample ClinicalModel Containing the ICGC micro-array cohort... |
| sampleCohortList | A Set of Example Patient Cohorts |
| sampleICGCmicro | A Sample SurvivalExperiment Containing Data from the ICGC... |
| samplePCOSPmodel | A Sample PCOSP Model Containing the ICGC micro-array cohort... |
| samplePCOSPpredList | Sample CohortList with PCOSP Risk Predictions |
| samplePCSIsurvExp | Sample SurvivalExperiment Containing the PCSI rna-sequencing... |
| sampleRGAmodel | Sample RGA Model Containing the ICGC micro-array cohort from... |
| sampleRLSmodel | Sample RLS Model Containing the ICGC micro-array cohort from... |
| sampleTrainedPCOSPmodel | A Sample Trained PCOSP Model Containing the ICGC micro-array... |
| 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-class | SurvivalExperiment Class |
| SurvivalModel | Constructor for a SurvivalModel Object. |
| SurvivalModel-class | A Generic Container for Storing Mathematical Models of... |
| trainData | Generic for Accessing the Training Data of an 'S4' Object |
| trainData-S4Model-method | Accessor for the Training Data in a 'S4Model' Object |
| trainData-set | Generic for Accessing the Training Data of an 'S4' Object |
| trainData-set-S4Model-method | Accessor for the Training Data in a 'S4Model' 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... |
| 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... |
| 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... |
| validateModel | Perform Validation on an 'S4' Object Representing a Trained... |
| validateModel-ClinicalModel-CohortList-method | Evaluate the Performance of a List of Trained KTSP Models... |
| validateModel-ClinicalModel-SurvivalExperiment-method | Validate a ClinicalModel object with a single... |
| validateModel-ConsensusMetaclusteringModel-ConsensusMetaclusteringModel-method | Compute the Inter-Cohort Cluster Correlation and Clustering... |
| validateModel-GeneFuModel-CohortList-method | Evaluate the Performance of a List of Trained KTSP Models... |
| validateModel-GeneFuModel-SurvivalExperiment-method | Validate a 'GenefuModel' object with a single... |
| validateModel-PCOSP_or_RLS_or_RGA-CohortList-method | Evaluate the Performance of a List of Trained KTSP Models... |
| validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method | Validate a PCOSP model with a single SurvivalExperiment... |
| validationData | Accessor for the 'validationData' slot of an 'S4' object |
| validationData-S4Model-method | Accessor for the 'validationData' slot of an 'S4Model' object |
| validationData-set | Generic for setting the 'validationData' slot on an 'S4'... |
| validationData-set-S4Model-List_or_list_or_NULL-method | Setter Method for the 'validationData' of an 'S4Model'... |
| validationData-set-SurvivalModel-CohortList-method | Setter for the 'validationData' slot of a 'SurvivalModel'... |
| validationData-SurvivalModel-method | Accessor for the 'validationData' slot of a 'SurvivalModel'... |
| validationStats | Accessor for the 'validationStats' slot of an 'S4' object |
| validationStats-S4Model-method | Acessor for the 'validationStats' slot of an 'S4Model' Object |
| validationStats-set | Setter for the 'validationStats' slot on an 'S4' object |
| validationStats-set-S4Model-DFrame_or_data.frame_data.table_or_NULL-method | Setter for the 'validationStats' slot on an 'S4Model' object |
| validationStats-set-SurvivalModel-data.frame-method | Setter for the validationStats slot of a 'SurvivalModel'... |
| validationStats-SurvivalModel-method | Accessor for the 'validationStats' slot of a 'SurvivalModel'... |
