initial upload, version 0.95alpha

1 files changed, 41 insertions, 0 deletions

diff --git a/mathfunc.h b/mathfunc.h
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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"
+
+
+using namespace std;
+
+double VectorVar (const gsl_vector *v);
+void CenterMatrix (gsl_matrix *G);
+void CenterMatrix (gsl_matrix *G, gsl_vector *w);
+void ScaleMatrix (gsl_matrix *G);
+double CenterVector (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);
+
+
+#endif