Merge branch 'master' of github.com:genetics-statistics/GEMMA

1 files changed, 101 insertions, 100 deletions

diff --git a/src/lmm.h b/src/lmm.h
index 9c3de9d..4d57ab1 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -19,120 +19,121 @@
 #ifndef __LMM_H__
 #define __LMM_H__
 
-#include "gsl/gsl_vector.h"
 #include "gsl/gsl_matrix.h"
-#include "param.h"
+#include "gsl/gsl_vector.h"
 #include "io.h"
+#include "param.h"
 
 using namespace std;
 
+#define LMM_BATCH_SIZE 10000 // 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;
+  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;
-	// WJA added
-	string file_oxford;
-
-	// 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.
-
-	// 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 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);
+  // 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;
+  // WJA added
+  string file_oxford;
+
+  // 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 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,
+                     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 &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
-
-