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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 __LM_H__
#define __LM_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 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_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
vector<int> indicator_idv; //indicator for individuals (phenotypes), 0 missing, 1 available for analysis
vector<int> indicator_snp; //sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis
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);
void WriteFiles ();
};
void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y, vector<pair<size_t, double> > &pos_loglr);
#endif
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