Added new files shared by Xiang via email on May 4, 2017.

1 files changed, 77 insertions, 0 deletions

diff --git a/src/ldr.h b/src/ldr.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 __LDR_H__                
+#define __LDR_H__
+
+#include <vector>
+#include <map>
+#include <gsl/gsl_rng.h>
+#include <gsl/gsl_randist.h>
+
+#ifdef FORCE_FLOAT
+#include "param_float.h"
+#else
+#include "param.h"
+#endif
+
+
+using namespace std;
+
+
+
+
+
+
+class LDR {
+
+public:	
+	// IO related parameters
+	int a_mode;	
+	size_t d_pace;
+	
+	string file_bfile;
+	string file_geno;
+	string file_out;
+	string path_out;
+		
+	// Summary statistics
+	size_t ni_total, ns_total;	//number of total individuals and snps
+	size_t ni_test, ns_test;	//number of individuals and snps used for analysis
+	size_t n_cvt;				//number of covariates
+	vector<int> indicator_idv;				//indicator for individuals (phenotypes), 0 missing, 1 available for analysis
+	vector<int> indicator_snp;				//sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis
+	
+	vector<SNPINFO> snpInfo;		//record SNP information
+	
+	// Not included in PARAM
+	gsl_rng *gsl_r; 	
+	
+	// Main Functions
+	void CopyFromParam (PARAM &cPar);
+	void CopyToParam (PARAM &cPar);
+	
+	void VB(const vector<vector<unsigned char> > &Xt, const gsl_matrix *W_gsl, const gsl_vector *y_gsl);
+};
+
+
+
+#endif
+
+