/* 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 . */ #ifndef __LDR_H__ #define __LDR_H__ #include #include #include #include #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 indicator_idv; //indicator for individuals (phenotypes), 0 missing, 1 available for analysis vector indicator_snp; //sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis vector 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 > &Xt, const gsl_matrix *W_gsl, const gsl_vector *y_gsl); }; #endif