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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 __LM_H__
#define __LM_H__
#include "gsl/gsl_vector.h"
#include "gsl/gsl_matrix.h"
#include "param.h"
#include "io.h"
using namespace std;
class LM {
public:
// IO-related parameters.
int a_mode; // Analysis mode: 50+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;
string file_gene;
// Summary statistics.
size_t ni_total, ni_test; // Number of individuals.
size_t ns_total, ns_test; // Number of SNPs.
size_t ng_total, ng_test; // Number of genes.
size_t n_cvt;
double time_opt; // Time spent.
// 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.
vector<SUMSTAT> sumStat; // Output SNPSummary Data.
// Main functions.
void CopyFromParam (PARAM &cPar);
void CopyToParam (PARAM &cPar);
void AnalyzeGene (const gsl_matrix *W, const gsl_vector *x);
void AnalyzePlink (const gsl_matrix *W, const gsl_vector *y);
void AnalyzeBimbam (const gsl_matrix *W, const gsl_vector *y);
// WJA added.
void Analyzebgen (const gsl_matrix *W, const gsl_vector *y);
void WriteFiles ();
};
void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y,
vector<pair<size_t, double> > &pos_loglr);
#endif
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