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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 __LMM_H__
#define __LMM_H__
#include "gsl/gsl_matrix.h"
#include "gsl/gsl_vector.h"
#include "io.h"
#include "param.h"
#include <functional>
#include <tuple>
using namespace std;
#define LMM_BATCH_SIZE 20000 // used for batch processing
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;
};
typedef std::tuple<string,std::vector<double> > SnpNameValues;
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;
// 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.
// 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.
set<string> setGWASnps; // 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 Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
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 set<string> gwasnps);
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,
const set<string> gwasnps);
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,
const set<string> gwasnps);
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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