net.maizegenetics.analysis.modelfitter

Class StepwiseAdditiveModelFitter

net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter

Direct Known Subclasses:

StepwiseAddDomModelFitter

public class StepwiseAdditiveModelFitter

A multi-threaded stepwise model fitter for additive only models. To use it first construct an object then call runAnalysis(). After the analysis has run, any of several reports will be available using getters. If a permutation test is requested it is run first. The analysis then fits SNPs consecutively, then rescans the full model to determine if any of the SNPs has a better choice given all the other SNPs in the model. As part of the rescan it calculates a support interval for each of the SNPs. Reports available include the steps taken to fit the model with sequential p-values, an anova with marginal p-values, a report of marker effects, a post-scan anova, post-scan marker effects, and a permutation report. It will also output a list of model residuals by chromosome. For each chromosome, it reports the residuals from a model that includes all effects, except the markers on that chromosome.

Field Detail

myGenoPheno

protected GenotypePhenotype myGenoPheno

myGenotype

protected GenotypeTable myGenotype

myPhenotype

protected Phenotype myPhenotype

dataAttributeList

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> dataAttributeList

covariateAttributeList

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> covariateAttributeList

factorAttributeList

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> factorAttributeList

dataname

protected java.lang.String dataname

y

protected kotlin.Array[] y

currentTraitName

protected java.lang.String currentTraitName

myModel

protected java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> myModel

numberOfBaseEffects

protected int numberOfBaseEffects

mySweepFast

protected SweepFastLinearModel mySweepFast

missing

protected BitSet missing

mySites

protected java.util.List<net.maizegenetics.analysis.modelfitter.AdditiveSite> mySites

nestingFactor

protected FactorModelEffect nestingFactor

nestingFactorLevelNames

protected java.util.List<java.lang.String> nestingFactorLevelNames

rescanAlpha

protected double rescanAlpha

allOfTheResidualPhenotypes

protected java.util.List<net.maizegenetics.phenotype.Phenotype> allOfTheResidualPhenotypes

numberOfPermutations

protected int numberOfPermutations

permutationAlpha

protected double permutationAlpha

enterLimit

protected double enterLimit

exitLimit

protected double exitLimit

useReferenceProbability

protected boolean useReferenceProbability

modelSelectionCriterion

protected net.maizegenetics.analysis.modelfitter.AdditiveSite.CRITERION modelSelectionCriterion

maxSitesInModel

protected int maxSitesInModel

createAnovaReport

protected boolean createAnovaReport

createPostScanEffectsReport

protected boolean createPostScanEffectsReport

createPreScanEffectsReport

protected boolean createPreScanEffectsReport

createStepReport

protected boolean createStepReport

createResidualsByChr

protected boolean createResidualsByChr

markerEffectReportBuilder

protected TableReportBuilder markerEffectReportBuilder

markerEffectCIReportBuilder

protected TableReportBuilder markerEffectCIReportBuilder

permutationReportBuilder

protected TableReportBuilder permutationReportBuilder

Constructor Detail

StepwiseAdditiveModelFitter

public StepwiseAdditiveModelFitter(GenotypePhenotype genopheno,
                                   java.lang.String datasetName)

Parameters:

genopheno - a GenotypePhenotype object

datasetName - a name for the genopheno

Throws:

IllegalArgumentException - if any phenotype data is missing

Method Detail

testPhenotypeForMissingData

public java.util.Optional<java.lang.String> testPhenotypeForMissingData(Phenotype pheno)

Parameters:

pheno - a Phenotype

Returns:

org.jetbrains.dokka.NodeRenderContent@461bf93: true, if there is missing data for any attribute, false otherwise

runAnalysis

public void runAnalysis()

This is called to run the analysis

fitModel

protected void fitModel()

baseModel

protected java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> baseModel(PhenotypeAttribute phenotypeBeingTested)

forwardStep

protected double forwardStep(double prevCriterionValue)

addToStepsReport

protected void addToStepsReport(int siteNumber,
                                SweepFastLinearModel theModel,
                                java.lang.String action,
                                kotlin.Array[] siteSSdf,
                                kotlin.Array[] errorSSdf,
                                double F,
                                double p)

scanToFindCI

protected java.util.List<kotlin.Array[]> scanToFindCI()

findCI

protected kotlin.Array[] findCI(ModelEffect me,
                                java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> theModel)

testAddedTerm

protected double testAddedTerm(int testedTerm,
                               AdditiveSite addedTerm,
                               java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> theModel)

bestTerm

protected AdditiveSite bestTerm(java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> baseModel,
                                kotlin.Array[] interval)

runPermutationTest

public void runPermutationTest()

addToAnovaReport

protected void addToAnovaReport(java.util.Optional<java.util.List> intervalList)

addToMarkerEffectReport

protected void addToMarkerEffectReport(boolean CI)

numberOfPermutations

public void numberOfPermutations(int nperm)

permutationAlpha

public void permutationAlpha(double alpha)

enterLimit

public void enterLimit(double limit)

exitLimit

public void exitLimit(double limit)

useReferenceProbability

public void useReferenceProbability(boolean useRefProb)

isNested

public void isNested(boolean nested)

nestingEffectName

public void nestingEffectName(java.lang.String factorName)

modelSelectionCriterion

public void modelSelectionCriterion(net.maizegenetics.analysis.modelfitter.AdditiveSite.CRITERION criterion)

maxSitesInModel

public void maxSitesInModel(int maxSites)

useResiduals

public void useResiduals(boolean useResid)

createAnovaReport

public void createAnovaReport(boolean createIt)

createPostScanEffectsReport

public void createPostScanEffectsReport(boolean createIt)

createPreScanEffectsReport

public void createPreScanEffectsReport(boolean createIt)

createResidualsByChr

public void createResidualsByChr(boolean createIt)

createStepReport

public void createStepReport(boolean createIt)

getAnovaReport

public TableReport getAnovaReport()

getAnovaReportWithCI

public TableReport getAnovaReportWithCI()

getMarkerEffectReport

public TableReport getMarkerEffectReport()

getMarkerEffectReportWithCI

public TableReport getMarkerEffectReportWithCI()

getResidualPhenotypesByChromosome

public java.util.List<net.maizegenetics.phenotype.Phenotype> getResidualPhenotypesByChromosome()

getPermutationReport

public TableReport getPermutationReport()

getSteps

public TableReport getSteps()

aic

public static double aic(double RSS,
                         int N,
                         double modelDf)

bic

public static double bic(double RSS,
                         int N,
                         double modelDf)

mbic

public static double mbic(double RSS,
                          int N,
                          double modelDf,
                          int numberOfSites)