org.metaqtl.util
Class OffspringManager

java.lang.Object
  org.metaqtl.util.OffspringManager

public final class OffspringManager
extends java.lang.Object

Class Description Here

Author:

Jean-Baptiste Veyrieras

Nested Class Summary

class

OffspringManager.HaldaneWaddingtonProportion

Constructor Summary

OffspringManager()

Method Summary

static double	fisherVariance(double r, int size, int type, int gen) Returns the inverse of the Fisher Information depending on the type of cross for a given recombination rate and a given population size.
static double	r2R(double r, int type, int gen) This routine returns the recombination rate r for a given value of the propertion of recombibant genotypes R according to the cross design.
static double	R2r(double R, int type, int gen) This routine returns the recombination rate r for a given value of the propertion of recombibant genotypes R according to the cross design.
static double	selfingIndividualInformation(OffspringManager.HaldaneWaddingtonProportion p) This routine returns the individual means amount of information for the given generation propertions for a self-fertilization design.
static void	selfingRecurrence(OffspringManager.HaldaneWaddingtonProportion p, double r) Given the current proportion C,D,E,F and G and the recombination rate r this routine computes the next generation proportions following the recurrence formula of Haldane and Waddington, 1931, Inbreeding and linkage, Genetics 16:357-374 (see section self-fertilization p358).

Methods inherited from class java.lang.Object

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

Constructor Detail

OffspringManager

public OffspringManager()

Method Detail

fisherVariance

public static double fisherVariance(double r,
                                    int size,
                                    int type,
                                    int gen)

Returns the inverse of the Fisher Information depending on the type of cross for a given recombination rate and a given population size.

Parameters:

r - the recombination rate estimate.

size -

type -

Returns:

the variance for the recombination rate estimate.

selfingRecurrence

public static void selfingRecurrence(OffspringManager.HaldaneWaddingtonProportion p,
                                     double r)

Given the current proportion C,D,E,F and G and the recombination rate r this routine computes the next generation proportions following the recurrence formula of Haldane and Waddington, 1931, Inbreeding and linkage, Genetics 16:357-374 (see section self-fertilization p358). Cn+1 = Cn + 0.5*En + 0.25*(1-r)^2*Fn + 0.25*r^2*Gn Dn+1 = p.D + 0.5*En + 0.25*r^2Fn + 0.25*(1-r)^2Gn En+1 = 0.5*En + 0.5*r*(1-r)*(Fn + Gn) Fn+1 = 0.5*(1-r)^2Fn + 0.5*r^2Gn Gn+1 = 0.5*r^2Fn + 0.5*(1-r)^2*Gn This also computes the next generation derivates dC,dD,dE,dF and dG which can be easily obtained from the above equations.

Parameters:

proportion -

selfingIndividualInformation

public static double selfingIndividualInformation(OffspringManager.HaldaneWaddingtonProportion p)

This routine returns the individual means amount of information for the given generation propertions for a self-fertilization design. This assumes that the 4 zygotic classes can be discriminated without uncertainty - i.e the case where markers are codominants.

Parameters:

p -

R2r

public static double R2r(double R,
                         int type,
                         int gen)

This routine returns the recombination rate r for a given value of the propertion of recombibant genotypes R according to the cross design. type : IBioCrossTypes.RILSe Recombinant Inbred Lines via selfing R = 2r/(1+2r) (Haldane and Waddington 1931) IBioCrossTypes.RILSi Recombinant Inbred Lines via sib-mating R = 4r/(1+6r) (Haldane and Waddington 1931) IBioCrossTypes.IRISe High Recombinant Inbred Lines via selfing R = 0.5(1-((1-2r)/(1+2r))(1-r)^t) (Winkler et al. 2003) IBioCrossTypes.IRISi High Recombinant Inbred Lines via sib-mating R = 0.5(1-((1-2r)/(1+6r))(1-r)^t) (Winkler et al. 2003)

Parameters:

R - the proportion of recombinant genotypes.

size - the population size.

type - the type of pedigree.

gen - the number of random mating generations (only for IRISi and IRISe).

Returns:

the recombination rate r.

r2R

public static double r2R(double r,
                         int type,
                         int gen)

This routine returns the recombination rate r for a given value of the propertion of recombibant genotypes R according to the cross design. type : IBioCrossTypes.RILSe Recombinant Inbred Lines via selfing R = 2r/(1+2r) (Haldane and Waddington 1931) IBioCrossTypes.RILSi Recombinant Inbred Lines via sib-mating R = 4r/(1+6r) (Haldane and Waddington 1931) IBioCrossTypes.IRISe High Recombinant Inbred Lines via selfing R = 0.5(1-((1-2r)/(1+2r))(1-r)^t) (Winkler et al. 2003) IBioCrossTypes.IRISi High Recombinant Inbred Lines via sib-mating R = 0.5(1-((1-2r)/(1+6r))(1-r)^t) (Winkler et al. 2003)

Parameters:

R - the proportion of recombinant genotypes.

size - the population size.

type - the type of pedigree.

gen - the number of random mating generations (only for IRISi and IRISe).

Returns:

the recombination rate r.