about summary refs log tree commit diff
path: root/src/lmm.h
diff options
context:
space:
mode:
Diffstat (limited to 'src/lmm.h')
-rw-r--r--src/lmm.h113
1 files changed, 67 insertions, 46 deletions
diff --git a/src/lmm.h b/src/lmm.h
index efbda4d..1e88cec 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -1,6 +1,6 @@
-/*
-	Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011  Xiang Zhou
+/* 
+    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
@@ -13,7 +13,7 @@
     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/>.
+    along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
 #ifndef __LMM_H__
@@ -21,22 +21,12 @@
 
 #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
-{
+class FUNC_PARAM {
 
 public:
 	bool calc_null;
@@ -48,15 +38,12 @@ public:
 	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
+	// 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;
@@ -75,42 +62,76 @@ public:
 	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 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
+	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
+        // Indicator for individuals (phenotypes): 0 missing, 1
+        // available for analysis.
+	vector<int> indicator_idv;				
 
-	vector<SNPINFO> snpInfo;		//record SNP information
+        // Sequence indicator for SNPs: 0 ignored because of (a) maf,
+        // (b) miss, (c) non-poly; 1 available for analysis.
+	vector<int> indicator_snp;
 
-	// Not included in PARAM
-	vector<SUMSTAT> sumStat;		//Output SNPSummary Data
+	vector<SNPINFO> snpInfo;  // Record SNP information.
 
-	// Main functions
+	// 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 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 &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 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);
+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
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-10-16 22:50:34 +0000