Man pages for bhklab/PanCuRx
Pancreatic Ductal Adenocarcinoma Tool-Kit

assignColDataColumnassignColDataColumn Assign a new column directly to the...
assignSubtypesAssign Sample Subtypes to an S4 Object
assignSubtypes-CohortList-list-methodAssign Subtype Annotations to a SurvivalExperiment Object
assignSubtypes-SurvivalExperiment-data.frame-methodAssign Subtype Annotations to a SurvivalExperiment Object
barPlotModelComparisonMake A Bar Plot Comparing Performance Between Two 'S4'...
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-methodMake a Bar Plot Comparison Model Performance Between a...
birnbaumPublished classifier gene signature for Birnbaum
chenPublished classifier gene signature for Chen
ClinicalModelConstructor for the ClinicalModel Class
ClinicalModel-classClinicalModel Class Definition
CohortListConstructor for the CohortList class, a specialized list for...
CohortList-classCohortList Class Definition
cohortSubtypeDFsA list of sample subtypes for the data in sampleCohortList
compareModelsCompare Two Mathematical Models Represented as 'S4' Objects
compareModels-ModelComparison-SurvivalModel-methodCompare Two 'SurivalModel' Objects, Returing A...
compareModels-SurvivalModel-SurvivalModel-methodCompare Two 'SurivalModel' Objects, Returing A...
ConsensusMetaclusteringModelConstructor for a 'ConsensusClusterModel' Object.
ConsensusMetaclusteringModel-classAn 'S4Model' Containing Molecular Data to be Consensus...
CoxModelCoxModel constructor
CoxModel-classCoxModel-class
CSPC_MAEA 'MultiAssayExperiment' containing cohorts of pancreatic...
densityPlotModelComparisonRender A Density Plot of Model Performance for an 'S4' Object
densityPlotModelComparison-PCOSP_or_RLS_or_RGA-PCOSP_or_RLS_or_RGA-methodRender a Density Plot Comparing Model Performance Between Two...
dot-findAllCohortPairsFind all non-self pair-wise combinations of cohorts
dot-randomSampleIndexGenerate a random sample from each group
dropNotCensoredRemove Censored Patient Samples from An 'S4' Object.
dropNotCensored-CohortList-methodRemove Censored Patients from Each 'SurvivalExperiemnt' in a...
dropNotCensored-SurvivalExperiment-methodRemove Censored Patients from A 'SurvivalExperiment' Object
existingClassifierDataexistingClassifierData
findCommonGenesFind the common genes in an 'S4' object.
findCommonGenes-CohortList-methodIntersect Gene Names for All 'SurvivalExperiments' in a...
findCommonGenes-MultiAssayExperiment-methodIntersect Gene Names for All 'experiments' in a...
findCommonSamplesFind Common Samples in a List-like S4 Object where The...
findCommonSamples-CohortList-methodFind Common Samples in a CohortList Object where The Columns...
forestPlotGenerate a forest plot from an 'S4' object
forestPlot-ModelComparison-methodRender a forest plot from the 'validationStats' slot of a...
forestPlot-PCOSP_or_ClinicalModel-methodRender a forest plot from the 'validationStats' slot of a...
GeneFuModel'GeneFuModel' Constructor Method
GeneFuModel-classA 'SurvivalModel' Sub-class Designed to Hold A Survival Model...
getModelSeedGeneric for retrieving the randomSeed parameter from a...
getModelSeed-SurvivalModel-methodMethod for retrieving the random seed used for training a...
getTopFeaturesGet the Top Predictive Features from an S4 Object
getTopFeatures-MultiAssayExperiment-methodGet the Top Ranked Features in a 'MultiAssayExperiment'...
getTopFeatures-PCOSP-methodGet the top features for classification using a PCOSP model...
getTopFeatures-SummarizedExperiment-methodGet the Top Ranked Features in a 'SummarizedExperiment'...
haiderSigScoresClassifier survival scores for Haider
hasColDataColumnsCheck for Column Names in the colData Slot of a...
merge-SurvivalExperiment-SurvivalExperiment-methodMerge two 'SurvivalExperiments', subsetting to shared rows...
ModelComparisonModelComparison Constructor
ModelComparison-classModelComparison Class Definition
modelParamsGeneric for Accessing the Model Parameters of an 'S4' Object
modelParams-S4Model-methodAccessor for the Model Parameters of an 'S4Model' Object
modelParams-setGeneric for Setting the Model Parameters of An 'S4' Object
modelParams-set-S4Model-List_or_list_or_NULL-methodSetter for the 'modelParams' of an 'S4Model'
modelsAccessor for the models slot of an 'S4' object
models-S4Model-methodGetter for the models slot of an 'S4Model' Object
models-setAccessor for the models slot of an 'S4' object
models-set-S4Model-List_or_list_or_NULL-methodSetter for the Models Slot of an 'S4Model' Object
models-set-SurvivalModel-SimpleList-methodSetter for the models slot of a 'SurvivalModel' object
models-SurvivalModel-methodGetter for the models slot of a 'SurvivalModel' object
NCSModel-classS4Model Class for Metaclustering Using Network Community...
NetworkCommunitySearchModelConstructor for a NetworkCommunitySearchModel (NCSModel)
normalize-data.frame_or_matrix-methodNormalize a 'data.frame' Object
normalize-DFrame-methodNormalize a S4 'DFrame' Object
normalize-MultiAssayExperiment-methodNormalize the 'assays' of a 'MutliAssayExperiment' Object
normalize-SummarizedExperiment-methodNormalize the 'assays' in a 'SummarizedExperiment' Object
normalsMAEA 'MultiAssayExperiment' containing cohorts of normal...
optimalKMinimizeAmbiguityPredict optimal K values by minimizing the difference between...
PCOSPPancreatic Cancer Overall Survival Predictor (PCOSP)...
PCOSP-classPancreatic Cancer Overall Survival Predictor (PCOSP) Class
PCOSP_or_ClinicalModel-classClass Union for PCOSP and ClinicalModel Types
PCOSP_or_RLS_or_RGA-classClass Union for PCOSP, RLSModel and RGAModel Types
plotNetworkGraphA Generic for Plotting a Network Graph From an S4 Object
plotNetworkGraph-NCSModel-methodPlot a Network Graph for a Classified NCSModel Object
plotROCPlot ROC curves for an 'S4' object
plotROC-PCOSP-methodPlot ROC curves for a 'PCOSP' model object.
plotSurvivalCurvesGeneric for Plotting Survival Curves from an 'S4' Object
plotSurvivalCurves-CoxModel-methodPlot Survival Curves from a Fit 'CoxModel' Object
predictClassesPredict Classes for New Data Based on a Train Classifier...
predictClasses-CohortList-ClinicalModel-methodUse a Clinical GLM to Predict Classes for a 'CohortList' of...
predictClasses-CohortList-GeneFuModel-methodUse a Gene Signature Based Prediciton Model from the 'genefu'...
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-methodPredict Survival Prognosis Classes and Risk Scores for A...
predictClasses-ConsensusMetaclusteringModel-ANY-methodCompute the Optimal Clustering Solution for a Trained...
predictClasses-NCSModel-ANY-methodPredict Metacluster Labels for a NetworkCommunitySearchModel
predictClasses-SurvivalExperiment-ClinicalModel-methodPredict Survival Prognosis Classes and Risk Scores for A...
predictClasses-SurvivalExperiment-GeneFuModel-methodUse a Gene Signature Based Prediciton Model from the 'genefu'...
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-methodPredict Survival Prognosis Classes and Risk Scores for A...
preprocessCaretPreprocess Data Using the 'caret::preProcess' method, then...
RandomGeneAssignmentModelRandomGeneAssignmentModel Constructor
RandomLabelShufflingModelRandomLabelShufflingModel Constructor
rankFeaturesRank the Features in a 'S4' Object
rankFeatures-MultiAssayExperiment-methodRank the Features in a 'MultiAssayExperiment' Object
rankFeatures-SummarizedExperiment-methodRank the Features in a 'SummarizedExperiment' Object
removeColDataFactorColumnsRemave any factor columns from the 'colData' of an 'S4'...
removeFactorColumnsConvert factor columns in a rectangular object
renameColDataColumnsRename the columns in the 'colData' slot, or do nothing if...
renameColumnsRename columns or do nothing if the names don't match
RGAModel-classRGAModel Class Definition
RLSModel-classRLSModel Class Definition
runGSEARun Gene Set Enrichment Analysis
runGSEA-PCOSP-data.frame-methodRun Gene Set Enrichment Analysis On A 'PCOSP' Model Object.
S4Model-classAn 'S4' Virtual Class For the Concept of a Statistical or ML...
sampleClinicalModelSample ClinicalModel Containing the ICGC micro-array cohort...
sampleCohortListA Set of Example Patient Cohorts
sampleICGCmicroA Sample SurvivalExperiment Containing Data from the ICGC...
samplePCOSPmodelA Sample PCOSP Model Containing the ICGC micro-array cohort...
samplePCOSPpredListSample CohortList with PCOSP Risk Predictions
samplePCSIsurvExpSample SurvivalExperiment Containing the PCSI rna-sequencing...
sampleRGAmodelSample RGA Model Containing the ICGC micro-array cohort from...
sampleRLSmodelSample RLS Model Containing the ICGC micro-array cohort from...
sampleTrainedPCOSPmodelA Sample Trained PCOSP Model Containing the ICGC micro-array...
sampleValPCOSPmodelSample Validated PCOSP Model for Plotting Examples
show-S4Model-methodShow method for Classes Inheriting from 'S4Model'
subset-CohortList-methodSubset method for a 'CohortList'
SurvivalExperimentConstructor for 'SurvivalExperiment' Class Builds a...
SurvivalExperiment-classSurvivalExperiment Class
SurvivalModelConstructor for a SurvivalModel Object.
SurvivalModel-classA Generic Container for Storing Mathematical Models of...
trainDataGeneric for Accessing the Training Data of an 'S4' Object
trainData-S4Model-methodAccessor for the Training Data in a 'S4Model' Object
trainData-setGeneric for Accessing the Training Data of an 'S4' Object
trainData-set-S4Model-methodAccessor for the Training Data in a 'S4Model' Object
trainModelTrain a Model Based on the Data in an S4 Object
trainModel-ClinicalModel-methodFit a GLM Using Clinical Predictors Specified in a...
trainModel-ConsensusMetaclusteringModel-methodTrain A ConsensusMetaclusteringModel
trainModel-CoxModel-methodFit Models to the trainData in a CoxModel Object
trainModel-GeneFuModel-methodTrain a GeneFuModel Object
trainModel-NCSModel-methodTrain a NetworkCommunitySearchModel
trainModel-PCOSP-methodTrain a PCOSP Model Based on The Data the assay...
trainModel-RGAModel-methodTrain a RGAModel Based on the Data in the assays slot.
trainModel-RLSModel-methodTrain a PCOSP Model Based on The Data the assay...
validateModelPerform Validation on an 'S4' Object Representing a Trained...
validateModel-ClinicalModel-CohortList-methodEvaluate the Performance of a List of Trained KTSP Models...
validateModel-ClinicalModel-SurvivalExperiment-methodValidate a ClinicalModel object with a single...
validateModel-ConsensusMetaclusteringModel-ConsensusMetaclusteringModel-methodCompute the Inter-Cohort Cluster Correlation and Clustering...
validateModel-GeneFuModel-CohortList-methodEvaluate the Performance of a List of Trained KTSP Models...
validateModel-GeneFuModel-SurvivalExperiment-methodValidate a 'GenefuModel' object with a single...
validateModel-PCOSP_or_RLS_or_RGA-CohortList-methodEvaluate the Performance of a List of Trained KTSP Models...
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-methodValidate a PCOSP model with a single SurvivalExperiment...
validationDataAccessor for the 'validationData' slot of an 'S4' object
validationData-S4Model-methodAccessor for the 'validationData' slot of an 'S4Model' object
validationData-setGeneric for setting the 'validationData' slot on an 'S4'...
validationData-set-S4Model-List_or_list_or_NULL-methodSetter Method for the 'validationData' of an 'S4Model'...
validationData-set-SurvivalModel-CohortList-methodSetter for the 'validationData' slot of a 'SurvivalModel'...
validationData-SurvivalModel-methodAccessor for the 'validationData' slot of a 'SurvivalModel'...
validationStatsAccessor for the 'validationStats' slot of an 'S4' object
validationStats-S4Model-methodAcessor for the 'validationStats' slot of an 'S4Model' Object
validationStats-setSetter for the 'validationStats' slot on an 'S4' object
validationStats-set-S4Model-DFrame_or_data.frame_data.table_or_NULL-methodSetter for the 'validationStats' slot on an 'S4Model' object
validationStats-set-SurvivalModel-data.frame-methodSetter for the validationStats slot of a 'SurvivalModel'...
validationStats-SurvivalModel-methodAccessor for the 'validationStats' slot of a 'SurvivalModel'...
bhklab/PanCuRx documentation built on Dec. 30, 2021, 4:59 p.m.