add GXE test

1 files changed, 14 insertions, 7 deletions

diff --git a/src/mathfunc.h b/src/mathfunc.h
index d0e1696..98c0e35 100644
--- a/src/mathfunc.h
+++ b/src/mathfunc.h
@@ -1,35 +1,39 @@
 /*
  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__                
+#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, gsl_vector *w);
-void ScaleMatrix (gsl_matrix *G);
+void CenterMatrix (gsl_matrix *G, const gsl_vector *w);
+void CenterMatrix (gsl_matrix *G, const gsl_matrix *W);
+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);
@@ -37,5 +41,8 @@ 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