From 0dd4e05fc8babc1517de1d7981a99ad0a5241a5e Mon Sep 17 00:00:00 2001
From: Peter Carbonetto
Date: Thu, 4 May 2017 14:43:12 -0500
Subject: Added new files shared by Xiang via email on May 4, 2017.

---
 src/bslmmdap.h | 101 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 src/bslmmdap.h

(limited to 'src/bslmmdap.h')

diff --git a/src/bslmmdap.h b/src/bslmmdap.h
new file mode 100644
index 0000000..ac78f97
--- /dev/null
+++ b/src/bslmmdap.h
@@ -0,0 +1,101 @@
+/*
+ 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 __BSLMMDAP_H__
+#define __BSLMMDAP_H__
+
+#include <vector>
+#include <map>
+#include <gsl/gsl_rng.h>
+#include <gsl/gsl_randist.h>
+
+#ifdef FORCE_FLOAT
+#include "param_float.h"
+#else
+#include "param.h"
+#endif
+
+
+using namespace std;
+
+
+
+
+
+
+class BSLMMDAP {
+
+public:
+	// IO related parameters
+	int a_mode;
+	size_t d_pace;
+
+	string file_bfile;
+	string file_geno;
+	string file_out;
+	string path_out;
+
+	// LMM related parameters
+	double pve_null;
+	double pheno_mean;
+
+	// BSLMM MCMC related parameters
+	long int randseed;
+	double trace_G;
+
+	HYPBSLMM cHyp_initial;
+
+	// Summary statistics
+	size_t ni_total, ns_total;	//number of total individuals and snps
+	size_t ni_test, ns_test;	//number of individuals and snps used for analysis
+
+	double h_min, h_max, rho_min, rho_max;
+	size_t h_ngrid, rho_ngrid;
+
+	double time_UtZ;
+	double time_Omega;		//time spent on optimization iterations
+	double time_Proposal;        //time spent on constructing the proposal distribution for gamma (i.e. lmm or lm analysis)
+	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
+
+	// Main Functions
+	void CopyFromParam (PARAM &cPar);
+	void CopyToParam (PARAM &cPar);
+
+	void WriteResult (const gsl_matrix *Hyper, const gsl_matrix *BF);
+	void WriteResult (const vector<string> &vec_rs, const gsl_matrix *Hyper, const gsl_vector *pip, const gsl_vector *coef);
+	double CalcMarginal (const gsl_vector *Uty, const gsl_vector *K_eval, const double sigma_b2, const double tau);
+	double CalcMarginal (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const gsl_vector *K_eval, const double sigma_a2, const double sigma_b2, const double tau);
+	double CalcPrior (class HYPBSLMM &cHyp);
+
+	void DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const gsl_vector *y);
+	void DAP_EstimateHyper (const size_t kc, const size_t kd, const vector<string> &vec_rs, const vector<double> &vec_sa2, const vector<double> &vec_sb2, const vector<double> &wab, const vector<vector<vector<double> > > &BF, gsl_matrix *Ac, gsl_matrix_int *Ad, gsl_vector_int *dlevel);
+
+};
+
+void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2, vector<double> &vec_sb2, vector<double> &vec_wab);
+void ReadFile_bf (const string &file_bf, vector<string> &vec_rs, vector<vector<vector<double> > > &BF);
+void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs, gsl_matrix *Ac, gsl_matrix_int *Ad, gsl_vector_int *dlevel, size_t &kc, size_t &kd);
+
+
+#endif
+
+
-- 
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