net.maizegenetics.analysis.imputation

Class FILLINImputationAccuracy

java.lang.Object

net.maizegenetics.analysis.imputation.FILLINImputationAccuracy

public class FILLINImputationAccuracy
extends Object

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

Author:

kls283

Field Summary

Fields

Modifier and Type	Field and Description
int[]	MAF

Constructor Summary

Constructors

Constructor and Description
FILLINImputationAccuracy(GenotypeTable unimp, GenotypeTable maskKey, GenotypeTable[] donor, double[] MAFClass, String outFileName, boolean verbose)
FILLINImputationAccuracy(GenotypeTable unimp, GenotypeTable maskKey, GenotypeTable[] donors, double propSitesMask, int depthToMask, double propDepthSitesToMask, String outFileName, double[] MAFClass, boolean verbose)
FILLINImputationAccuracy(GenotypeTable unimp, GenotypeTable maskKey, GenotypeTable[] donor, String outFileName, boolean verbose)
FILLINImputationAccuracy(GenotypeTable unimp, GenotypeTable maskKey, String outFileName, boolean verbose)

Method Summary

Modifier and Type	Method and Description
double	calcAccuracy(GenotypeTable imputed, double runtime)
static double[]	compareAlignment(GenotypeTable impGT, GenotypeTable keyGT, String taxaPrefix) Deprecated. a similar method is need in the core part of accuracy.
static int[]	compareAlignment(String origFile, String maskFile, String impFile, boolean noMask) Deprecated.
GenotypeTable	initiateAccuracy()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAF

public int[] MAF

Constructor Detail

FILLINImputationAccuracy

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

FILLINImputationAccuracy

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

FILLINImputationAccuracy

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

FILLINImputationAccuracy

public FILLINImputationAccuracy(GenotypeTable unimp,
                                GenotypeTable maskKey,
                                GenotypeTable[] donor,
                                double[] MAFClass,
                                String outFileName,
                                boolean verbose)

Method Detail

initiateAccuracy

public GenotypeTable initiateAccuracy()

calcAccuracy

public double calcAccuracy(GenotypeTable imputed,
                           double runtime)

compareAlignment

@Deprecated
public static int[] compareAlignment(String origFile,
                                                 String maskFile,
                                                 String impFile,
                                                 boolean noMask)

Deprecated.

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

compareAlignment

@Deprecated
public static double[] compareAlignment(GenotypeTable impGT,
                                                    GenotypeTable keyGT,
                                                    String taxaPrefix)

Deprecated. a similar method is need in the core part of accuracy.

Calculates proportion imputed, homozygous proportion right, heterozygous proportion right

Parameters:

impGT -

keyGT -

Returns: