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/*
Genome-wide Efficient Mixed Model Association (GEMMA)
Copyright (C) 2011 Xiang Zhou
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __MATHFUNC_H__
#define __MATHFUNC_H__
#include "gsl/gsl_vector.h"
#include "gsl/gsl_matrix.h"
#include "Eigen/Dense"
using namespace std;
using namespace Eigen;
double VectorVar (const gsl_vector *v);
void CenterMatrix (gsl_matrix *G);
void CenterMatrix (gsl_matrix *G, const gsl_vector *w);
void CenterMatrix (gsl_matrix *G, const gsl_matrix *W);
void StandardizeMatrix (gsl_matrix *G);
double ScaleMatrix (gsl_matrix *G);
double CenterVector (gsl_vector *y);
void CenterVector (gsl_vector *y, const gsl_matrix *W);
void StandardizeVector (gsl_vector *y);
void CalcUtX (const gsl_matrix *U, gsl_matrix *UtX);
void CalcUtX (const gsl_matrix *U, const gsl_matrix *X, gsl_matrix *UtX);
void CalcUtX (const gsl_matrix *U, const gsl_vector *x, gsl_vector *Utx);
double CalcHWE (const size_t n_hom1, const size_t n_hom2, const size_t n_ab);
void Kronecker(const gsl_matrix *K, const gsl_matrix *V, gsl_matrix *H);
void KroneckerSym(const gsl_matrix *K, const gsl_matrix *V, gsl_matrix *H);
double UcharToDouble02(const unsigned char c);
unsigned char Double02ToUchar(const double dosage);
void uchar_matrix_get_row (const vector<vector<unsigned char> > &X, const size_t i_row, VectorXd &x_row);
#endif
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