umcg.genetica.io.trityper.util

Class DetermineLD

java.lang.Object

umcg.genetica.io.trityper.util.DetermineLD

public class DetermineLD
extends Object

Author:

lude

Field Summary

Fields

Modifier and Type	Field and Description
double	h11
double	h12
double	h21
double	h22
static int	INCLUDE_CASES
static int	INCLUDE_CASES_AND_CONTROLS
static int	INCLUDE_CONTROLS
int	nrCalledGenotypes
static int	RETURN_D_PRIME
static int	RETURN_R_SQUARED

Constructor Summary

Constructors

Constructor and Description
DetermineLD() Creates a new instance of DetermineLD

Method Summary

Modifier and Type	Method and Description
Pair<Double,Double>	getLD(SNP snpX, SNP snpY, TriTyperGenotypeData genotypeData, int individualsToInclude, boolean print)
double	getRSquared(SNP snpX, SNP snpY, TriTyperGenotypeData genotypeData, int returnType, int individualsToInclude, boolean print)

Methods inherited from class java.lang.Object

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

Field Detail

INCLUDE_CASES_AND_CONTROLS

public static final int INCLUDE_CASES_AND_CONTROLS

See Also:

Constant Field Values

INCLUDE_CASES

public static final int INCLUDE_CASES

See Also:

Constant Field Values

INCLUDE_CONTROLS

public static final int INCLUDE_CONTROLS

See Also:

Constant Field Values

RETURN_R_SQUARED

public static final int RETURN_R_SQUARED

See Also:

Constant Field Values

RETURN_D_PRIME

public static final int RETURN_D_PRIME

See Also:

Constant Field Values

h11

public double h11

h12

public double h12

h21

public double h21

h22

public double h22

nrCalledGenotypes

public int nrCalledGenotypes

Constructor Detail

DetermineLD

public DetermineLD()

Creates a new instance of DetermineLD

Method Detail

getRSquared

public double getRSquared(SNP snpX,
                          SNP snpY,
                          TriTyperGenotypeData genotypeData,
                          int returnType,
                          int individualsToInclude,
                          boolean print)

getLD

public Pair<Double,Double> getLD(SNP snpX,
                                 SNP snpY,
                                 TriTyperGenotypeData genotypeData,
                                 int individualsToInclude,
                                 boolean print)