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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 __VC_H__
#define __VC_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 VC_PARAM
{
public:
const gsl_matrix *K;
const gsl_matrix *W;
const gsl_vector *y;
gsl_matrix *P;
gsl_vector *Py;
gsl_matrix *KPy_mat;
gsl_matrix *PKPy_mat;
gsl_matrix *Hessian;
bool noconstrain;
};
class VC {
public:
// IO related parameters
size_t a_mode;
string file_cat;
string file_beta;
string file_cor;
string file_mq;
string file_ms;
string file_out;
string path_out;
set<string> setSnps;
size_t ni_total_ref, ns_total_ref, ns_pair;
size_t ni_total, ns_total, ns_test;
size_t n_vc;
double pve_total, se_pve_total;
vector<double> v_sigma2;
vector<double> v_se_sigma2;
vector<double> v_pve;
vector<double> v_se_pve;
vector<double> v_traceG;
vector<double> v_beta;
vector<double> v_se_beta;
size_t crt;
double window_cm, window_bp, window_ns;
double time_UtX;
double time_opt;
// Main functions
void CopyFromParam (PARAM &cPar);
void CopyToParam (PARAM &cPar);
void WriteFile_qs (const gsl_vector *s_vec, const gsl_vector *q_vec, const gsl_vector *qvar_vec, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat);
void CalcVChe (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
void CalcVCreml (const bool noconstrain, const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
void CalcVCacl (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
};
void CalcVCss(const gsl_matrix *Vq, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat, const gsl_vector *q_vec, const gsl_vector *s_vec, const double df, vector<double> &v_pve, vector<double> &v_se_pve, double &pve_total, double &se_pve_total, vector<double> &v_sigma2, vector<double> &v_se_sigma2, vector<double> &v_enrich, vector<double> &v_se_enrich);
bool BimbamXwz (const string &file_geno, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const vector<size_t> &vec_cat, const gsl_vector *w, const gsl_vector *z, size_t ns_test, gsl_matrix *XWz);
bool PlinkXwz (const string &file_bed, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const vector<size_t> &vec_cat, const gsl_vector *w, const gsl_vector *z, size_t ns_test, gsl_matrix *XWz);
bool MFILEXwz (const size_t mfile_mode, const string &file_mfile, const int display_pace, vector<int> &indicator_idv, vector<vector<int> > &mindicator_snp, const vector<size_t> &vec_cat, const gsl_vector *w, const gsl_vector *z, gsl_matrix *XWz);
bool BimbamXtXwz (const string &file_geno, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const gsl_matrix *XWz, size_t ns_test, gsl_matrix *XtXWz);
bool PlinkXtXwz (const string &file_bed, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const gsl_matrix *XWz, size_t ns_test, gsl_matrix *XtXWz);
bool MFILEXtXwz (const size_t mfile_mode, const string &file_mfile, const int display_pace, vector<int> &indicator_idv, vector<vector<int> > &mindicator_snp, const gsl_matrix *XWz, gsl_matrix *XtXWz);
void CalcCIss(const gsl_matrix *Xz, const gsl_matrix *XWz, const gsl_matrix *XtXWz, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat, const gsl_vector *w, const gsl_vector *z, const gsl_vector *s_vec, const vector<size_t> &vec_cat, const vector<double> &v_pve, vector<double> &v_se_pve, double &pve_total, double &se_pve_total, vector<double> &v_sigma2, vector<double> &v_se_sigma2, vector<double> &v_enrich, vector<double> &v_se_enrich);
#endif
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