net.maizegenetics.analysis.imputation

Class FILLINImputationAccuracy

net.maizegenetics.analysis.imputation.FILLINImputationAccuracy

public class FILLINImputationAccuracy

A class to mask input files, hold information related to accuracy calculation, and calculate accuracy for FILLINImputationPlugin

Field Detail

MAF

public kotlin.Array[] MAF

Constructor Detail

FILLINImputationAccuracy

public FILLINImputationAccuracy(GenotypeTable unimp,
                                GenotypeTable maskKey,
                                GenotypeTable[] donors,
                                double propSitesMask,
                                int depthToMask,
                                double propDepthSitesToMask,
                                java.lang.String outFileName,
                                kotlin.Array[] MAFClass,
                                boolean verbose)

FILLINImputationAccuracy

public FILLINImputationAccuracy(GenotypeTable unimp,
                                GenotypeTable maskKey,
                                java.lang.String outFileName,
                                boolean verbose)

FILLINImputationAccuracy

public FILLINImputationAccuracy(GenotypeTable unimp,
                                GenotypeTable maskKey,
                                GenotypeTable[] donor,
                                java.lang.String outFileName,
                                boolean verbose)

FILLINImputationAccuracy

public FILLINImputationAccuracy(GenotypeTable unimp,
                                GenotypeTable maskKey,
                                GenotypeTable[] donor,
                                kotlin.Array[] MAFClass,
                                java.lang.String outFileName,
                                boolean verbose)

Method Detail

initiateAccuracy

public GenotypeTable initiateAccuracy()

calcAccuracy

public double calcAccuracy(GenotypeTable imputed,
                           double runtime)

compareAlignment

public static kotlin.Array[] compareAlignment(java.lang.String origFile,
                                              java.lang.String maskFile,
                                              java.lang.String impFile,
                                              boolean noMask)

Legacy approach for measuring accuracy, but need to maintain some tests.

compareAlignment

public static kotlin.Array[] compareAlignment(GenotypeTable impGT,
                                              GenotypeTable keyGT,
                                              java.lang.String taxaPrefix)

Calculates proportion imputed, homozygous proportion right, heterozygous proportion right

Parameters:

impGT -

keyGT -

Returns:

org.jetbrains.dokka.NodeRenderContent@4e729e7d: