initial upload, version 0.95alpha

1 files changed, 110 insertions, 0 deletions

diff --git a/lmm.h b/lmm.h
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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 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
+	
+	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);
+	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 WriteFiles ();
+	
+	void CalcRLWald (const double &lambda, const FUNC_PARAM &params, double &beta, double &se, double &p_wald);
+	void CalcRLScore (const double &l, const FUNC_PARAM &params, 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 &params, 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
+
+