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Diffstat (limited to 'prdt.h')
| -rw-r--r-- | prdt.h | 81 |
1 files changed, 0 insertions, 81 deletions
@@ -1,81 +0,0 @@ -/* - 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 - - - - - - - |