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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 <fstream>
#include <iostream>
#include <sstream>
#include <algorithm>
#include <cmath>
#include <cstring>
#include <ctime>
#include <iomanip>
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
// #include "Eigen/Dense"
#include "gsl/gsl_blas.h"
#include "gsl/gsl_cdf.h"
#include "gsl/gsl_eigen.h"
#include "gsl/gsl_linalg.h"
#include "gsl/gsl_matrix.h"
#include "gsl/gsl_randist.h"
#include "gsl/gsl_roots.h"
#include "gsl/gsl_vector.h"
#include "lapack.h"
#include "ldr.h"
#include "lm.h"
#include "mathfunc.h"
#include "param.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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