Files in bhklab/PanCuRx

Pancreatic Ductal Adenocarcinoma Tool-Kit

R/class-ClinicalModel.R R/class-CohortList.R R/class-ConsensusMetaclusteringModel.R R/class-CoxModel.R R/class-GeneFuModel.R R/class-ModelComparison.R R/class-NCSModel.R R/class-PCOSP.R R/class-RGAModel.R R/class-RLSModel.R R/class-S4Model.R R/class-SurvivalExperiment.R R/class-SurvivalModel.R R/classUnions.R R/data.R R/globals.R R/methods-assignSubtypes.R R/methods-barPlotModelComparison.R R/methods-coerce.R R/methods-compareModels.R R/methods-densityPlotModelComparison.R R/methods-dropNotCensored.R R/methods-findCommonGenes.R R/methods-findCommonSamples.R R/methods-forestPlot.R R/methods-getTopFeatures.R R/methods-merge.R R/methods-normalize.R R/methods-plotNetworkGraph.R R/methods-plotROC.R R/methods-plotSurvivalCurves.R R/methods-predictClasses.R R/methods-rankFeatures.R R/methods-runGSEA.R R/methods-subset.R R/methods-trainModel.R R/methods-validateModel.R R/utilities.R man/CSPC_MAE.Rd man/ClinicalModel-class.Rd man/ClinicalModel.Rd man/CohortList-class.Rd man/CohortList.Rd man/ConsensusMetaclusteringModel-class.Rd man/ConsensusMetaclusteringModel.Rd man/CoxModel-class.Rd man/CoxModel.Rd man/GeneFuModel-class.Rd man/GeneFuModel.Rd man/ModelComparison-class.Rd man/ModelComparison.Rd man/NCSModel-class.Rd man/NetworkCommunitySearchModel.Rd man/PCOSP-class.Rd man/PCOSP.Rd man/PCOSP_or_ClinicalModel-class.Rd man/PCOSP_or_RLS_or_RGA-class.Rd man/RGAModel-class.Rd man/RLSModel-class.Rd man/RandomGeneAssignmentModel.Rd man/RandomLabelShufflingModel.Rd man/S4Model-class.Rd man/SurvivalExperiment-class.Rd man/SurvivalExperiment.Rd man/SurvivalModel-class.Rd man/SurvivalModel.Rd man/assignColDataColumn.Rd man/assignSubtypes-CohortList-list-method.Rd man/assignSubtypes-SurvivalExperiment-data.frame-method.Rd man/assignSubtypes.Rd man/barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method.Rd man/barPlotModelComparison.Rd man/birnbaum.Rd man/chen.Rd man/cohortSubtypeDFs.Rd man/compareModels-ModelComparison-SurvivalModel-method.Rd man/compareModels-SurvivalModel-SurvivalModel-method.Rd man/compareModels.Rd man/densityPlotModelComparison-PCOSP_or_RLS_or_RGA-PCOSP_or_RLS_or_RGA-method.Rd man/densityPlotModelComparison.Rd man/dot-findAllCohortPairs.Rd man/dot-randomSampleIndex.Rd man/dropNotCensored-CohortList-method.Rd man/dropNotCensored-SurvivalExperiment-method.Rd man/dropNotCensored.Rd man/existingClassifierData.Rd man/findCommonGenes-CohortList-method.Rd man/findCommonGenes-MultiAssayExperiment-method.Rd man/findCommonGenes.Rd man/findCommonSamples-CohortList-method.Rd man/findCommonSamples.Rd man/forestPlot-ModelComparison-method.Rd man/forestPlot-PCOSP_or_ClinicalModel-method.Rd man/forestPlot.Rd man/getModelSeed-SurvivalModel-method.Rd man/getModelSeed.Rd man/getTopFeatures-MultiAssayExperiment-method.Rd man/getTopFeatures-PCOSP-method.Rd man/getTopFeatures-SummarizedExperiment-method.Rd man/getTopFeatures.Rd man/haiderSigScores.Rd man/hasColDataColumns.Rd man/merge-SurvivalExperiment-SurvivalExperiment-method.Rd man/modelParams-S4Model-method.Rd man/modelParams-set-S4Model-List_or_list_or_NULL-method.Rd man/modelParams-set.Rd man/modelParams.Rd man/models-S4Model-method.Rd man/models-SurvivalModel-method.Rd man/models-set-S4Model-List_or_list_or_NULL-method.Rd man/models-set-SurvivalModel-SimpleList-method.Rd man/models-set.Rd man/models.Rd man/normalize-DFrame-method.Rd man/normalize-MultiAssayExperiment-method.Rd man/normalize-SummarizedExperiment-method.Rd man/normalize-data.frame_or_matrix-method.Rd man/normalsMAE.Rd man/optimalKMinimizeAmbiguity.Rd man/plotNetworkGraph-NCSModel-method.Rd man/plotNetworkGraph.Rd man/plotROC-PCOSP-method.Rd man/plotROC.Rd man/plotSurvivalCurves-CoxModel-method.Rd man/plotSurvivalCurves.Rd man/predictClasses-CohortList-ClinicalModel-method.Rd man/predictClasses-CohortList-GeneFuModel-method.Rd man/predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method.Rd man/predictClasses-ConsensusMetaclusteringModel-ANY-method.Rd man/predictClasses-NCSModel-ANY-method.Rd man/predictClasses-SurvivalExperiment-ClinicalModel-method.Rd man/predictClasses-SurvivalExperiment-GeneFuModel-method.Rd man/predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method.Rd man/predictClasses.Rd man/preprocessCaret.Rd man/rankFeatures-MultiAssayExperiment-method.Rd man/rankFeatures-SummarizedExperiment-method.Rd man/rankFeatures.Rd man/removeColDataFactorColumns.Rd man/removeFactorColumns.Rd man/renameColDataColumns.Rd man/renameColumns.Rd man/runGSEA-PCOSP-data.frame-method.Rd man/runGSEA.Rd man/sampleClinicalModel.Rd man/sampleCohortList.Rd man/sampleICGCmicro.Rd man/samplePCOSPmodel.Rd man/samplePCOSPpredList.Rd man/samplePCSIsurvExp.Rd man/sampleRGAmodel.Rd man/sampleRLSmodel.Rd man/sampleTrainedPCOSPmodel.Rd man/sampleValPCOSPmodel.Rd man/show-S4Model-method.Rd man/subset-CohortList-method.Rd man/trainData-S4Model-method.Rd man/trainData-set-S4Model-method.Rd man/trainData-set.Rd man/trainData.Rd man/trainModel-ClinicalModel-method.Rd man/trainModel-ConsensusMetaclusteringModel-method.Rd man/trainModel-CoxModel-method.Rd man/trainModel-GeneFuModel-method.Rd man/trainModel-NCSModel-method.Rd man/trainModel-PCOSP-method.Rd man/trainModel-RGAModel-method.Rd man/trainModel-RLSModel-method.Rd man/trainModel.Rd man/validateModel-ClinicalModel-CohortList-method.Rd man/validateModel-ClinicalModel-SurvivalExperiment-method.Rd man/validateModel-ConsensusMetaclusteringModel-ConsensusMetaclusteringModel-method.Rd man/validateModel-GeneFuModel-CohortList-method.Rd man/validateModel-GeneFuModel-SurvivalExperiment-method.Rd man/validateModel-PCOSP_or_RLS_or_RGA-CohortList-method.Rd man/validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method.Rd man/validateModel.Rd man/validationData-S4Model-method.Rd man/validationData-SurvivalModel-method.Rd man/validationData-set-S4Model-List_or_list_or_NULL-method.Rd man/validationData-set-SurvivalModel-CohortList-method.Rd man/validationData-set.Rd man/validationData.Rd man/validationStats-S4Model-method.Rd man/validationStats-SurvivalModel-method.Rd man/validationStats-set-S4Model-DFrame_or_data.frame_data.table_or_NULL-method.Rd man/validationStats-set-SurvivalModel-data.frame-method.Rd man/validationStats-set.Rd man/validationStats.Rd tests/testthat.R tests/testthat/test-ClinicalModel-constructor.R tests/testthat/test-ClinicalModel-trainModel-predictClasses-validateModel.R tests/testthat/test-GeneFuModel-constructor.R tests/testthat/test-GeneFuModel-trainModel-predictClasses-validateModel.R tests/testthat/test-ModelComparions-constructor.R tests/testthat/test-PCOSP-trainModel-predictClasses-validateModel.R tests/testthat/test-RGAModel-constructor.R tests/testthat/test-RLSModel-constructor.R tests/testthat/test-SurvivalExperiment-coercion.R tests/testthat/test-SurvivalExperiment-constructor.R tests/testthat/test-SurvivalModel-accessors.R tests/testthat/test-SurvivalModel-constructor.R vignettes/CSPC_model_analysis.rmd vignettes/PCOSP_model_analysis.Rmd vignettes/PDATK_introduction.rmd