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/*
Genome-wide Efficient Mixed Model Association (GEMMA)
Copyright (C) 2011-2017 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 __BSLMMDAP_H__
#define __BSLMMDAP_H__
#include <vector>
#include <map>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include "param.h"
using namespace std;
class BSLMMDAP {
public:
// IO-related parameters.
int a_mode;
size_t d_pace;
string file_bfile;
string file_geno;
string file_out;
string path_out;
// LMM related parameters
double pve_null;
double pheno_mean;
// BSLMM MCMC related parameters
long int randseed;
double trace_G;
HYPBSLMM cHyp_initial;
// 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
double h_min, h_max, rho_min, rho_max;
size_t h_ngrid, rho_ngrid;
double time_UtZ;
double time_Omega; //time spent on optimization iterations
double time_Proposal; //time spent on constructing the proposal distribution for gamma (i.e. lmm or lm analysis)
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
// Main Functions
void CopyFromParam (PARAM &cPar);
void CopyToParam (PARAM &cPar);
void WriteResult (const gsl_matrix *Hyper, const gsl_matrix *BF);
void WriteResult (const vector<string> &vec_rs, const gsl_matrix *Hyper, const gsl_vector *pip, const gsl_vector *coef);
double CalcMarginal (const gsl_vector *Uty, const gsl_vector *K_eval, const double sigma_b2, const double tau);
double CalcMarginal (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const gsl_vector *K_eval, const double sigma_a2, const double sigma_b2, const double tau);
double CalcPrior (class HYPBSLMM &cHyp);
void DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const gsl_vector *y);
void DAP_EstimateHyper (const size_t kc, const size_t kd, const vector<string> &vec_rs, const vector<double> &vec_sa2, const vector<double> &vec_sb2, const vector<double> &wab, const vector<vector<vector<double> > > &BF, gsl_matrix *Ac, gsl_matrix_int *Ad, gsl_vector_int *dlevel);
};
void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2, vector<double> &vec_sb2, vector<double> &vec_wab);
void ReadFile_bf (const string &file_bf, vector<string> &vec_rs, vector<vector<vector<double> > > &BF);
void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs, gsl_matrix *Ac, gsl_matrix_int *Ad, gsl_vector_int *dlevel, size_t &kc, size_t &kd);
#endif
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