Relationship matrix regression. More...

#include <MuGen.h>

Inheritance diagram for BetaGrpPC:

Collaboration diagram for BetaGrpPC:

Public Member Functions
	BetaGrpPC ()
	Default constructor.

	BetaGrpPC (const Grp &rsp, const string &predFlNam, const string &evFlNam, const size_t &Npred, RanIndex &up, const int &nThr)
	Constructor with a prior index. More...

	BetaGrpPC (const Grp &rsp, const string &predFlNam, const string &evFlNam, const size_t &Npred, RanIndex &low, RanIndex &up, const int &nThr)
	Constructor with a prior index and replication. More...

	BetaGrpPC (const Grp &rsp, const string &predFlNam, const string &evFlNam, const size_t &Npred, RanIndex &up, const string &outFlNam, const int &nThr)
	Constructor with a prior index, replication and output file name. More...

	BetaGrpPC (const Grp &rsp, const string &predFlNam, const string &evFlNam, const size_t &Npred, RanIndex &low, RanIndex &up, const string &outFlNam, const int &nThr)
	Constructor with a prior index and replication. More...

virtual	~BetaGrpPC ()
	Destructor.

	BetaGrpPC (const BetaGrpPC &mG)
	Copy constructor. More...

BetaGrpPC &	operator= (const BetaGrpPC &mG)
	Assignment operator. More...

Public Member Functions inherited from BetaGrpFt
	BetaGrpFt ()
	Default constructor.

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const int &nThr)
	Simple constructor. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, RanIndex &up, const int &nThr)
	Simple constructor with a prior index. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, RanIndex &low, RanIndex &up, const int &nThr)
	Simple constructor with a prior index and replication. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const string &outFlNam, const int &nThr)
	Simple constructor with output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, RanIndex &up, const string &outFlNam, const int &nThr)
	Simple constructor with a prior index and output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, RanIndex &low, RanIndex &up, const string &outFlNam, const int &nThr)
	Simple constructor with a prior index, replication and output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, const int &nThr)
	Missing data constructor. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, RanIndex &up, const int &nThr)
	Missing data constructor with a prior index. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, RanIndex &low, RanIndex &up, const int &nThr)
	Missing data constructor with a prior index and replication. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, const string &outFlNam, const int &nThr)
	Missing data constructor with output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, RanIndex &up, const string &outFlNam, const int &nThr)
	Missing data constructor with a prior index and output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, RanIndex &low, RanIndex &up, const string &outFlNam, const int &nThr)
	Missing data constructor with a prior index, replication and output file name. More...

	BetaGrpFt (const Grp &rsp, const SigmaI &SigI, const string &predFlNam, const size_t &Npred, const double &Nmul, const double &rSqMax, RanIndex &up, const string &outFlNam, const int &nThr)
	Selection constructor. More...

	BetaGrpFt (const Grp &rsp, const SigmaI &SigI, const string &predFlNam, const size_t &Npred, const double &Nmul, const double &rSqMax, RanIndex &low, RanIndex &up, const string &outFlNam, const int &nThr)
	Selection constructor with replication. More...

	BetaGrpFt (const Grp &rsp, const SigmaI &SigI, const string &predFlNam, const size_t &Npred, const double &Nmul, const double &rSqMax, const double &absLab, RanIndex &up, const string &outFlNam, const int &nThr)
	Selection constructor with missing predictor data. More...

	BetaGrpFt (const Grp &rsp, const SigmaI &SigI, const string &predFlNam, const size_t &Npred, const double &Nmul, const double &rSqMax, const double &absLab, RanIndex &low, RanIndex &up, const string &outFlNam, const int &nThr)
	Selection constructor with missing predictor data and replication. More...

virtual	~BetaGrpFt ()
	Destructor.

	BetaGrpFt (const BetaGrpFt &mG)
	Copy constructor. More...

BetaGrpFt &	operator= (const BetaGrpFt &mG)
	Assignment operator. More...

virtual const gsl_matrix *	fMat () const
	Access to the fitted value matrix. More...

void	save (const SigmaI &SigI)
	Store samples. More...

void	dump ()
	Dump to a file. More...

double	lnOddsRat (const Grp &y, const SigmaI &SigI, const size_t i) const
	Log-odds ratio. More...

void	update (const Grp &dat, const SigmaI &SigIm)
	Gaussian likelihood, improper prior. More...

void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm)
	Student- \(t\) likelihood, improper prior. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const SigmaI &SigIp)
	Gaussian likelihood, 0-mean Gaussian prior. More...

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const SigmaI &SigIp)
	Student- \(t\) likelihood, 0-mean Gaussian prior. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const Qgrp &qPr, const SigmaI &SigIp)
	Gaussian likelihood, 0-mean Student- \(t\) prior. More...

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const Qgrp &qPr, const SigmaI &SigIp)
	Student- \(t\) likelihood, 0-mean Student- \(t\) prior. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const Grp &muPr, const SigmaI &SigIp)
	Gaussian likelihood, non-zero mean Gaussian prior. More...

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const Grp &muPr, const SigmaI &SigIp)
	Student- \(t\) likelihood, non-zero mean Gaussian prior. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const Grp &muPr, const Qgrp &qPr, const SigmaI &SigIp)
	Gaussian likelihood, non-zero mean Student- \(t\) prior. More...

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const Grp &muPr, const Qgrp &qPr, const SigmaI &SigIp)
	Student- \(t\) likelihood, non-zero mean Student- \(t\) prior. More...

Public Member Functions inherited from Grp
virtual	~Grp ()
	Destructor.

virtual void	save ()
	Save to pre-specified file. More...

virtual void	save (const string &outFlNam)
	Save to file. More...

virtual void	save (const string &outMuFlNam, const string &outSigFlNam, const SigmaI &SigI)
	Joint save. More...

virtual void	save (const Grp &y, const SigmaI &SigI)
	Save with data and inverse-covariance. More...

void	mhlSave (const string &outFlNam, const SigmaI SigI)
	Save Mahalanobis distance. More...

const vector< MVnorm * > &	dataVec () const
	Get vector of row pointers. More...

virtual const gsl_matrix *	dMat () const
	Access the value matrix. More...

const size_t	Ndata () const
	Get number of rows. More...

const size_t	phenD () const
	Get number of traits. More...

const MVnorm *	operator[] (const size_t i) const
	Subscript operator. More...

MVnorm *	operator[] (const size_t i)
	Subscript operator. More...

virtual MuGrp	mean (RanIndex &grp)
	Group mean. More...

virtual const MuGrp	mean (RanIndex &grp) const
	Group mean. More...

virtual MuGrp	mean (RanIndex &grp, const Qgrp &q)
	Group weighted mean. More...

virtual const MuGrp	mean (RanIndex &grp, const Qgrp &q) const
	Group weighted mean. More...

void	center ()
	Center the value matrix. More...

Additional Inherited Members
Protected Member Functions inherited from BetaGrpFt
virtual void	_updateFitted ()
	Update fitted values.

void	_rankPred (const gsl_matrix y, const SigmaI &SigI, gsl_vector XtX, gsl_permutation *prm)
	Rank predictors. More...

void	_rankPred (const gsl_matrix y, const SigmaI &SigI, const double &absLab, gsl_vector XtX, gsl_permutation *prm)
	Rank predictors with missing data. More...

void	_ldToss (const gsl_vector var, const gsl_permutation prm, const double &rSqMax, const size_t &Npck, vector< vector< size_t > > &idx, vector< vector< size_t > > &rLd, gsl_matrix *Xpck)
	Testing candidates for correlation. More...

virtual double	_MGkernel (const Grp &dat, const SigmaI &SigI) const
	Gaussian kernel. More...

virtual double	_MGkernel (const Grp &dat, const SigmaI &SigI, const size_t &prInd) const
	Gaussian kernel dropping one predictor. More...

Protected Member Functions inherited from Grp
	Grp ()

Protected Attributes inherited from BetaGrpFt
vector< vector< double > >	_fittedEach
	Partial fitted value matrices. More...

gsl_matrix *	_fittedAll
	Matrix of fitted values. More...

gsl_matrix *	_valueSum
	Sample storage matrix. More...

gsl_matrix *	_Xmat
	Predictor matrix. More...

int	_nThr
	Number of threads.

double	_numSaves
	Number of saves. More...

Protected Attributes inherited from Grp
vector< MVnorm * >	_theta
	Vector of pointers to value rows. More...

gsl_matrix *	_valueMat
	Value matrix. More...

RanIndex *	_lowLevel
	Lower level index. More...

RanIndex *	_upLevel
	Upper level index. More...

vector< gsl_rng * >	_rV
	Vector of PNG pointers. More...

string	_outFlNam
	Name of the output file.

Detailed Description

Relationship matrix regression.

Implements regression models with principal components of a relationship matrix as predictors. Only principal vectors with non-zero eigenvalues are used. If the likelihood and the prior are Gaussian, and the prior mean is zero, this is equivalent to the "mixed model" in packages like EMMA and TASSEL. Because the PC vectors are orthonormal there are some speed-ups in initialization. The updates are handled by the same internal row classes as in BetaGrpFt.

Constructor & Destructor Documentation

◆ BetaGrpPC() [1/5]

BetaGrpPC::BetaGrpPC	(	const Grp &	rsp,
		const string &	predFlNam,
		const string &	evFlNam,
		const size_t &	Npred,
		RanIndex &	up,
		const int &	nThr
	)

Constructor with a prior index.

Reads principal vectors and eigen-values from files. Number of rows of the predictor is equal to the number of rows in the response (no replication).

Parameters

[in]	Grp&	data for initialization
[in]	string&	PC vector file name
[in]	string&	eigen-value file name
[in]	size_t&	number of predictors
[in]	RanIndex&	prior index
[in]	int&	number of threads

◆ BetaGrpPC() [2/5]

BetaGrpPC::BetaGrpPC	(	const Grp &	rsp,
		const string &	predFlNam,
		const string &	evFlNam,
		const size_t &	Npred,
		RanIndex &	low,
		RanIndex &	up,
		const int &	nThr
	)

Constructor with a prior index and replication.

Reads principal vectors and eigen-values from files. Number of rows of the predictor is equal to the number of groups in the lower (data) index. The number of rows in the response is equal to the number of elements in the low index.

Parameters

[in]	Grp&	data for initialization
[in]	string&	PC vector file name
[in]	string&	eigen-value file name
[in]	size_t&	number of predictors
[in]	RanIndex&	lower-level (replicate) index
[in]	RanIndex&	prior index
[in]	int&	number of threads

◆ BetaGrpPC() [3/5]

BetaGrpPC::BetaGrpPC	(	const Grp &	rsp,
		const string &	predFlNam,
		const string &	evFlNam,
		const size_t &	Npred,
		RanIndex &	up,
		const string &	outFlNam,
		const int &	nThr
	)

Constructor with a prior index, replication and output file name.

Reads principal vectors and eigen-values from files. Number of rows of the predictor is equal to the number of groups in the lower (data) index. The number of rows in the response is equal to the number of elements in the low index.

Parameters

[in]	Grp&	data for initialization
[in]	string&	PC vector file name
[in]	string&	eigen-value file name
[in]	size_t&	number of predictors
[in]	RanIndex&	lower-level (replicate) index
[in]	RanIndex&	prior index
[in]	string&	output file name
[in]	int&	number of threads

◆ BetaGrpPC() [4/5]

BetaGrpPC::BetaGrpPC	(	const Grp &	rsp,
		const string &	predFlNam,
		const string &	evFlNam,
		const size_t &	Npred,
		RanIndex &	low,
		RanIndex &	up,
		const string &	outFlNam,
		const int &	nThr
	)

Constructor with a prior index and replication.

Reads principal vectors and eigen-values from files. Number of rows of the predictor is equal to the number of groups in the lower (data) index. The number of rows in the response is equal to the number of elements in the low index.

Parameters

[in]	Grp&	data for initialization
[in]	string&	PC vector file name
[in]	string&	eigen-value file name
[in]	size_t&	number of predictors
[in]	RanIndex&	lower-level (replicate) index
[in]	RanIndex&	prior index
[in]	string&	output file name
[in]	int&	number of threads

◆ BetaGrpPC() [5/5]

BetaGrpPC::BetaGrpPC ( const BetaGrpPC & mG )

Copy constructor.

Parameters

[in] BetaGrpPC& object to be copied

Member Function Documentation

◆ operator=()

BetaGrpPC & BetaGrpPC::operator= ( const BetaGrpPC & mG )

Assignment operator.

Parameters

[in] BetaGrpPC& object to be copied

Returns: BetaGrpPC& target object

The documentation for this class was generated from the following files:

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BetaGrpPC() [1/5]

◆ BetaGrpPC() [2/5]

◆ BetaGrpPC() [3/5]

◆ BetaGrpPC() [4/5]

◆ BetaGrpPC() [5/5]

Member Function Documentation

◆ operator=()