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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
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