version 0.95alpha

1 files changed, 0 insertions, 111 deletions

diff --git a/lmm.h b/lmm.h
deleted file mode 100644
index 45f9b72..0000000
--- a/lmm.h
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
-	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;
-	
-	// 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
-
-