/* Genome-wide Efficient Mixed Model Association (GEMMA) Copyright (C) 2011-2017, 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 . */ #ifndef __MATHFUNC_H__ #define __MATHFUNC_H__ #include "Eigen/Dense" #include "gsl/gsl_matrix.h" #include "gsl/gsl_vector.h" 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> &X, const size_t i_row, VectorXd &x_row); #endif