version 0.95alpha

1 files changed, 81 insertions, 0 deletions

diff --git a/src/prdt.h b/src/prdt.h
new file mode 100644
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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 __PRDT_H__                
+#define __PRDT_H__
+
+
+#include <vector>
+#include <map>
+#include <string.h>
+#include "gsl/gsl_vector.h"
+#include "gsl/gsl_matrix.h"
+
+#ifdef FORCE_FLOAT
+#include "param_float.h"
+#else
+#include "param.h"
+#endif
+
+using namespace std;
+
+class PRDT {
+	
+public:
+	// IO related parameters
+	size_t a_mode;
+	size_t d_pace;
+	
+	string file_bfile;
+	string file_geno;
+	string file_out;
+	string path_out;
+	
+	vector<vector<int> > indicator_pheno;
+	vector<int> indicator_cvt;
+	vector<int> indicator_idv;
+	vector<SNPINFO> snpInfo;
+	map<string, double> mapRS2est;
+	
+	size_t n_ph;
+	size_t np_obs, np_miss;
+	size_t ns_total;
+	size_t ns_test;
+	
+	double time_eigen;
+	
+	// Main functions
+	void CopyFromParam (PARAM &cPar);
+	void CopyToParam (PARAM &cPar);
+	void WriteFiles (gsl_vector *y_prdt);
+	void WriteFiles (gsl_matrix *Y_full);
+	void AddBV (gsl_matrix *G, const gsl_vector *u_hat, gsl_vector *y_prdt);
+	void AnalyzeBimbam (gsl_vector *y_prdt);
+	void AnalyzePlink (gsl_vector *y_prdt);
+	void MvnormPrdt (const gsl_matrix *Y_hat, const gsl_matrix *H, gsl_matrix *Y_full);
+};
+
+
+#endif
+
+
+
+
+
+
+