Files in andrewhaoyu/TOP

Two-stage Polytomous Logistic regression

R/CheckControlTumor.R R/CleanNotEnoughSubtype.R R/CompleteCasesScoreTestSupport.R R/CountTumorNumber.R R/EMScoreTestSupport.R R/EMStep.R R/EMStepScoreTestSupport.R R/EMStepScoreTestSupportMixedModel.R R/EMmvpoly.R R/EMmvpolySelfDesign.R R/FillandMatch.R R/FirstStageTest.R R/GenerateCompleteYPheno.R R/GenerateCovarName.R R/GenerateFirstStageMat.R R/GenerateFreqTable.R R/GenerateGlobalTest.R R/GenerateSecondStageMat.R R/GenerateSelfCovarName.R R/GenerateSelfFirstStageMat.R R/GenerateSelfSecondStageMat.R R/GenerateSelfXALL.R R/GenerateSubtypesName.R R/GenerateTumorCharacterCat.R R/GenerateXAll.R R/GenerateZDesignCombination.R R/HypothesisTest.R R/InitialSetup.R R/LoglikelihoodAIC.R R/LogoddsMetaAnalysis.R R/MVpolySelfDesign.R R/MetaPfunction.R R/Mvpoly.R R/OneStepMLE.R R/OneStepMleScoreSupport.R R/ProbFitting.R R/ScoreTest.R R/ScoreTestMixedModel.r R/ScoreTestSelfDesign.R R/ScoreTestSupport.r R/ScoreTestSupportMixedModel.R R/ScoreTestSupportMixedModelSelfDesign.R R/ScoreTestSupportSelfDesign.R R/SecondStageTest.R R/SelfFirstStageTest.R R/StartValueFunction.R R/StepScoreTestSupportMixedModel.R R/TakeoutIntercept.R R/TwoStageModel.R R/ZDesigntoZall.R R/ZSelfDesigntoZall.R R/check_mem.R R/convert.R R/display_95CI_p.R R/error_f.R R/generate_z_design_matrix.R R/get_fine_mapping_id.R R/p_value_function.R R/startend.R R/utils.R README.md inst/TOP.Rmd inst/TOP.pdf man/CheckControlTumor.Rd man/CompleteCasesScoreTestSupport.Rd man/ComputeLogLikelihood.Rd man/CountCovarNumber.Rd man/DisplayFirstStageTestResult.Rd man/DisplayFixedScoreTestResult.Rd man/DisplayIndTestResult.Rd man/DisplayMixedScoreTestResult.Rd man/DisplaySecondStageTestResult.Rd man/EMScoreTestSupport.Rd man/EMStep.Rd man/EMStepScoreTestSupport.Rd man/EMStepScoreTestSupportMixedModel.Rd man/EMmvpoly.Rd man/EMmvpolySelfDesign.Rd man/FillandMatch.Rd man/FirstStageTest.Rd man/GenerateCompleteXCovariates.Rd man/GenerateCompleteYPheno.Rd man/GenerateCovarName.Rd man/GenerateFirstStageMat.Rd man/GenerateFreqTable.Rd man/GenerateGlobalTest.Rd man/GenerateMissingPosition.Rd man/GenerateSecondStageMat.Rd man/GenerateSelfCovarName.Rd man/GenerateSelfFirstStageMat.Rd man/GenerateSelfSecondStageMat.Rd man/GenerateSelfXAll.Rd man/GenerateSubtypesName.Rd man/GenerateTumorCharacterCat.Rd man/GenerateXAll.Rd man/GenerateZDesignAdditive.Rd man/GenerateZDesignBaselineonly.Rd man/GenerateZDesignCombination.Rd man/GenerateZDesignNamesAdditive.Rd man/GenerateZDesignPairwiseInteraction.Rd man/GenerateZDesignSaturated.Rd man/GenerateZstandard.Rd man/GlobalTestForAssoc.Rd man/GlobalTestForHeter.Rd man/IndividualHeterTest.Rd man/InitialSetup.Rd man/LogLikelihoodwithAIC.Rd man/LogoddsMetaAnalysis.Rd man/MetaFixedPfunction_temp.Rd man/MetaMixedPfunction.Rd man/MetaMixedPfunction_temp.Rd man/MetaPfunction.Rd man/Mvpoly.Rd man/MvpolySelfDesign.Rd man/OneStepMLE.Rd man/OneStepMleScoreTestSupport.Rd man/ProbFitting.Rd man/PvalueFunction.Rd man/ScoreGlobalMixedTestForAssoc.Rd man/ScoreGlobalTestForAssoc.Rd man/ScoreMetaAnalysis.Rd man/ScoreMixedGlobalTestForAssoc.Rd man/ScoreMixedGlobalTestForHeter.Rd man/ScoreTest.Rd man/ScoreTestMixedModel.Rd man/ScoreTestSelfDesign.Rd man/ScoreTestSupport.Rd man/ScoreTestSupportMixedModel.Rd man/ScoreTestSupportMixedModelSelfDesign.Rd man/ScoreTestSupportSelfDesign.Rd man/SecondStageTest.Rd man/SelfFirstStageTest.Rd man/StartValueFunction.Rd man/StepScoreTestSupportMixedModel.Rd man/SummaryResult.Rd man/TakeoutIntercept.Rd man/TwoStageModel.Rd man/ZDesigntoZall.Rd man/ZSelfDesigntoZall.Rd man/convert.Rd man/error_f.Rd man/get_fine_mapping_id.Rd man/ls.objects.Rd man/lsos.Rd man/rowmatch.Rd man/startend.Rd tests/example_for_bill.R tests/test_code.R tests/test_example.R tests/test_onco.R