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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/>.
*/
#include <iostream>
#include <fstream>
#include <sstream>
#include <iomanip>
#include <cmath>
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <ctime>
#include <cstring>
#include <algorithm>
#include "gsl/gsl_vector.h"
#include "gsl/gsl_matrix.h"
#include "gsl/gsl_linalg.h"
#include "gsl/gsl_blas.h"
#include "gsl/gsl_eigen.h"
#include "gsl/gsl_randist.h"
#include "gsl/gsl_cdf.h"
#include "gsl/gsl_roots.h"
#include "Eigen/Dense"
#include "lapack.h"
#include "param.h"
#include "ldr.h"
#include "lm.h"
#include "mathfunc.h"
using namespace std;
using namespace Eigen;
void LDR::CopyFromParam (PARAM &cPar) {
a_mode=cPar.a_mode;
d_pace=cPar.d_pace;
file_bfile=cPar.file_bfile;
file_geno=cPar.file_geno;
file_out=cPar.file_out;
path_out=cPar.path_out;
ni_total=cPar.ni_total;
ns_total=cPar.ns_total;
ni_test=cPar.ni_test;
ns_test=cPar.ns_test;
n_cvt=cPar.n_cvt;
indicator_idv=cPar.indicator_idv;
indicator_snp=cPar.indicator_snp;
snpInfo=cPar.snpInfo;
return;
}
void LDR::CopyToParam (PARAM &cPar) {
return;
}
//X is a p by n matrix.
void LDR::VB (const vector<vector<unsigned char> > &Xt,
const gsl_matrix *W_gsl, const gsl_vector *y_gsl) {
// Save gsl_vector and gsl_matrix into Eigen library formats.
MatrixXd W(W_gsl->size1, W_gsl->size2);
VectorXd y(y_gsl->size);
VectorXd x_col(y_gsl->size);
double d;
for (size_t i=0; i<W_gsl->size1; i++) {
d=gsl_vector_get(y_gsl, i);
y(i)=d;
for (size_t j=0; j<W_gsl->size2; j++) {
W(i,j)=gsl_matrix_get(W_gsl, i, j);
}
}
// Initial VB values by lm.
cout<<indicator_snp[0]<<" "<<indicator_snp[1]<<" "<<indicator_snp[2]<<endl;
uchar_matrix_get_row (Xt, 0, x_col);
for (size_t j=0; j<10; j++) {
cout<<x_col(j)<<endl;
}
// Run VB iterations.
// TO DO.
// Save results.
// TO DO.
return;
}
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