1 files changed, 0 insertions, 75 deletions
diff --git a/lm.h b/lm.h
deleted file mode 100644
index ceec060..0000000
--- a/lm.h
+++ /dev/null
@@ -1,75 +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 __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 path_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