net.maizegenetics.analysis.modelfitter

Class StepwiseOLSModelFitter

net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter

public class StepwiseOLSModelFitter

Constructor Detail

StepwiseOLSModelFitter

public StepwiseOLSModelFitter(GenotypePhenotype genoPheno,
                              java.lang.String datasetName)

Method Detail

setModelType

public void setModelType(net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter.MODEL_TYPE modelType)

runAnalysis

public DataSet runAnalysis()

fitModel

public void fitModel()

removeCollinearMarkers

public java.util.ArrayList<java.lang.Double> removeCollinearMarkers(boolean removeCollinearMarker)

scanAndFindCI

public void scanAndFindCI()

forwardStep

public boolean forwardStep()

backwardStep

public boolean backwardStep()

runPermutationTestNoMissingData

public void runPermutationTestNoMissingData()

getPermutationReport

public TableReport getPermutationReport()

createReportRowsFromCurrentModel

public java.util.LinkedList<kotlin.Array[]> createReportRowsFromCurrentModel(SweepFastLinearModel sflm)

createReportRowsFromCurrentModelAfterScanCI

public java.util.LinkedList<kotlin.Array[]> createReportRowsFromCurrentModelAfterScanCI(SweepFastLinearModel sflm)

createReportFromCurrentModel

public Datum createReportFromCurrentModel(SweepFastLinearModel sflm)

createReportFromCurrentModelWithCI

public Datum createReportFromCurrentModelWithCI(SweepFastLinearModel sflm)

appendAnovaResults

public void appendAnovaResults(SweepFastLinearModel sflm)

appendAnovaResultsWithCI

public void appendAnovaResultsWithCI(SweepFastLinearModel sflm)

getAnovaReport

public TableReport getAnovaReport()

getAnovaReportWithCI

public TableReport getAnovaReportWithCI()

getMarkerEffectReport

public TableReport getMarkerEffectReport()

getMarkerEffectReportWithCI

public TableReport getMarkerEffectReportWithCI()

appendSiteEffectEstimates

public void appendSiteEffectEstimates(SweepFastLinearModel sflm)

appendSiteEffectEstimatesWithCI

public void appendSiteEffectEstimatesWithCI(SweepFastLinearModel sflm)

generateChromosomeResidualsFromCurrentModel

public Phenotype generateChromosomeResidualsFromCurrentModel()

setEnterlimits

public void setEnterlimits(kotlin.Array[] enterlimits)

setExitlimits

public void setExitlimits(kotlin.Array[] exitlimits)

setEnterlimit

public void setEnterlimit(double enterlimit)

setExitlimit

public void setExitlimit(double exitlimit)

setMaxNumberOfMarkers

public void setMaxNumberOfMarkers(int maxNumberOfMarkers)

setNestingEffectIndex

public void setNestingEffectIndex(int nestingFactorIndex)

setNested

public void setNested(boolean isNested)

setNumberOfPermutations

public void setNumberOfPermutations(int numberOfPermutations)

setAlpha

public void setAlpha(double alpha)