Man pages for andrewhaoyu/TOP
Two-stage Polytomous Logistic regression

CheckControlTumor	Check whether control subtypes tumor characteristics is NA
CompleteCasesScoreTestSupport	Title
ComputeLogLikelihood	Title
convert	Convert the impute 2 data into the 0, 1, 2 coding
CountCovarNumber	Count variable number
DisplayFirstStageTestResult	Display the first stage parameters
DisplayFixedScoreTestResult	Calcualte the fixed effect score test p value based on score...
DisplayIndTestResult	Calculate the individual test p value
DisplayMixedScoreTestResult	Calculate the mixed effect model p value based on score and...
DisplaySecondStageTestResult	DisplaySecondStageTestResult
EMmvpoly	Two-stage model MLE estimation with EM algorithm
EMmvpolySelfDesign	Two stage model with self design second stage matrix
EMScoreTestSupport	Title
EMStep	Title
EMStepScoreTestSupport	Title
EMStepScoreTestSupportMixedModel	Title
error_f	Title
FillandMatch	Title
FirstStageTest	Title
GenerateCompleteXCovariates	Title
GenerateCompleteYPheno	Title
GenerateCovarName	Title
GenerateFirstStageMat	Title
GenerateFreqTable	Title
GenerateGlobalTest	Title
GenerateMissingPosition	Title
GenerateSecondStageMat	Title
GenerateSelfCovarName	Title
GenerateSelfFirstStageMat	Title
GenerateSelfSecondStageMat	Title
GenerateSelfXAll	Title
GenerateSubtypesName	Title
GenerateTumorCharacterCat	Title
GenerateXAll	Title
GenerateZDesignAdditive	Title
GenerateZDesignBaselineonly	Title
GenerateZDesignCombination	Generate the three Z design matrix given the tumor...
GenerateZDesignNamesAdditive	Title
GenerateZDesignPairwiseInteraction	Title
GenerateZDesignSaturated	Title
GenerateZstandard	Generate the combinations of all the tumor characteristics.
get_fine_mapping_id	Title
GlobalTestForAssoc	Title
GlobalTestForHeter	Title
IndividualHeterTest	Title
InitialSetup	Title
LogLikelihoodwithAIC	Title
LogoddsMetaAnalysis	Title
ls.objects	Title
lsos	Title
MetaFixedPfunction_temp	Title
MetaMixedPfunction	Title
MetaMixedPfunction_temp	Title
MetaPfunction	Title
Mvpoly	Title
MvpolySelfDesign	Title
OneStepMLE	Title
OneStepMleScoreTestSupport	Title
ProbFitting	Title
PvalueFunction	Title
rowmatch	TBD
ScoreGlobalMixedTestForAssoc	Title
ScoreGlobalTestForAssoc	Title
ScoreMetaAnalysis	Title
ScoreMixedGlobalTestForAssoc	Title
ScoreMixedGlobalTestForHeter	Title
ScoreTest	ScoreTest
ScoreTestMixedModel	Title
ScoreTestSelfDesign	Title
ScoreTestSupport	Title
ScoreTestSupportMixedModel	Generate the support list for score test To construct a score...
ScoreTestSupportMixedModelSelfDesign	Title
ScoreTestSupportSelfDesign	Title
SecondStageTest	Title
SelfFirstStageTest	Title
startend	Title
StartValueFunction	Title
StepScoreTestSupportMixedModel	Title
SummaryResult	Title
TakeoutIntercept	Title
TwoStageModel	Two-stage polytomous logistic regression
ZDesigntoZall	Title
ZSelfDesigntoZall	Title