net.maizegenetics.analysis.imputation

Class ImputeCrossProgeny

net.maizegenetics.analysis.imputation.ImputeCrossProgeny

public class ImputeCrossProgeny

Method Detail

setPlotList

public void setPlotList(java.util.List<kotlin.Array[]> plotList)

imputeAll

public void imputeAll()

imputeCrossFromParents

public kotlin.Array[] imputeCrossFromParents(java.lang.String progeny,
                                             kotlin.Array[] hap0,
                                             kotlin.Array[] hap1)

improveImputedProgenyStates

public void improveImputedProgenyStates()

imputeCrossFromParentsUsingProbabilities

public kotlin.Array[] imputeCrossFromParentsUsingProbabilities(java.lang.String progeny,
                                                               kotlin.Array[] hapProb0,
                                                               kotlin.Array[] hapProb1,
                                                               kotlin.Array[] probObsGivenState)

updateStateObsCounts

public void updateStateObsCounts(kotlin.Array[] counts,
                                 kotlin.Array[] hap0,
                                 kotlin.Array[] hap1,
                                 kotlin.Array[] states,
                                 java.lang.String progenyName)

fillgaps

public void fillgaps(kotlin.Array[] states)

setParentCallInputFilename

public void setParentCallInputFilename(java.lang.String parentCallFilename)

setMyGenotype

public void setMyGenotype(GenotypeTable myGenotype)

setParentage

public void setParentage(java.lang.String parentageFilename)

setHaplotypeMap

public void setHaplotypeMap(java.lang.String parentHaplotypeFilename)

setImputedGenotypeOutFilename

public void setImputedGenotypeOutFilename(java.lang.String imputedGenotypeOutFilename)

setParentcallOutFilename

public void setParentcallOutFilename(java.lang.String parentcallOutFilename)

setPhasedParentOutFilename

public void setPhasedParentOutFilename(java.lang.String phasedParentOutFilename)

writeBreakpointFile

public void writeBreakpointFile(GenotypeTable imputedGenotypes,
                                java.lang.String outFilename)