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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 __LDR_H__
#define __LDR_H__
#include <vector>
#include <map>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include "param.h"
using namespace std;
class LDR {
public:
// IO-related parameters.
int a_mode;
size_t d_pace;
string file_bfile;
string file_geno;
string file_out;
string path_out;
// Summary statistics.
size_t ni_total, ns_total; // Total number of individuals & SNPs.
size_t ni_test, ns_test; // Number of individuals & SNPs used
// for analysis
size_t n_cvt; // Number of covariates.
// Indicator for individuals (phenotypes): 0 missing, 1
// available for analysis.
vector<int> indicator_idv;
// Sequence indicator for SNPs: 0 ignored because of (a) maf,
// (b) miss, (c) non-poly; 1 available for analysis.
vector<int> indicator_snp;
vector<SNPINFO> snpInfo; // Record SNP information.
// Not included in PARAM.
gsl_rng *gsl_r;
// Main functions.
void CopyFromParam (PARAM &cPar);
void CopyToParam (PARAM &cPar);
void VB(const vector<vector<unsigned char> > &Xt,
const gsl_matrix *W_gsl, const gsl_vector *y_gsl);
};
#endif
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