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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 __LMM_H__
#define __LMM_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 FUNC_PARAM
{
public:
bool calc_null;
size_t ni_test;
size_t n_cvt;
const gsl_vector *eval;
const gsl_matrix *Uab;
const gsl_vector *ab;
size_t e_mode;
};
class LMM {
public:
// IO related parameters
int a_mode; //analysis mode, 1/2/3/4 for Frequentist tests
size_t d_pace; //display pace
string file_bfile;
string file_geno;
string file_out;
string path_out;
string file_gene;
// WJA added
string file_oxford;
// LMM related parameters
double l_min;
double l_max;
size_t n_region;
double l_mle_null;
double logl_mle_H0;
// 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_UtX; //time spent on optimization iterations
double time_opt; //time spent on optimization iterations
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 *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Utx, const gsl_matrix *W, const gsl_vector *x);
void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
// WJA added
void Analyzebgen (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
void AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y, const gsl_vector *env);
void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y, const gsl_vector *env);
void WriteFiles ();
void CalcRLWald (const double &lambda, const FUNC_PARAM ¶ms, double &beta, double &se, double &p_wald);
void CalcRLScore (const double &l, const FUNC_PARAM ¶ms, double &beta, double &se, double &p_score);
};
void MatrixCalcLR (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const double l_min, const double l_max, const size_t n_region, vector<pair<size_t, double> > &pos_loglr);
void CalcLambda (const char func_name, FUNC_PARAM ¶ms, const double l_min, const double l_max, const size_t n_region, double &lambda, double &logf);
void CalcLambda (const char func_name, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double l_min, const double l_max, const size_t n_region, double &lambda, double &logl_H0);
void CalcPve (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double lambda, const double trace_G, double &pve, double &pve_se);
void CalcLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double lambda, double &vg, double &ve, gsl_vector *beta, gsl_vector *se_beta);
#endif
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