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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 __MVLMM_H__
#define __MVLMM_H__
#include "gsl/gsl_vector.h"
#include "gsl/gsl_matrix.h"
#ifdef FORCE_FLOAT
#include "param_float.h"
#include "io_float.h"
#else
#include "param.h"
#include "io.h"
#endif
using namespace std;
class MVLMM {
public:
// IO related parameters
int a_mode; //analysis mode, 1/2/3/4 for Frequentist tests
size_t d_pace; //display pace
string file_bfile;
string file_geno;
string file_oxford;
string file_out;
string path_out;
// MVLMM related parameters
double l_min;
double l_max;
size_t n_region;
double logl_remle_H0, logl_mle_H0;
vector<double> Vg_remle_null, Ve_remle_null, Vg_mle_null, Ve_mle_null;
vector<double> VVg_remle_null, VVe_remle_null, VVg_mle_null, VVe_mle_null;
vector<double> beta_remle_null, se_beta_remle_null, beta_mle_null, se_beta_mle_null;
double p_nr;
size_t em_iter, nr_iter;
double em_prec, nr_prec;
size_t crt;
// Summary statistics
size_t ni_total, ni_test; //number of individuals
size_t ns_total, ns_test; //number of snps
size_t n_cvt;
size_t n_ph;
double time_UtX; //time spent on optimization iterations
double time_opt; //time spent on optimization iterations
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
vector<MPHSUMSTAT> sumStat; //Output SNPSummary Data
// Main functions
void CopyFromParam (PARAM &cPar);
void CopyToParam (PARAM &cPar);
void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
void Analyzebgen (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const gsl_vector *env);
void AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const gsl_vector *env);
void WriteFiles ();
};
void CalcMvLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const size_t em_iter, const size_t nr_iter, const double em_prec, const double nr_prec, const double l_min, const double l_max, const size_t n_region, gsl_matrix *V_g, gsl_matrix *V_e, gsl_matrix *B, gsl_matrix *se_B);
#endif
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