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+/*
+	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 __PARAM_H__                
+#define __PARAM_H__
+
+#include <vector>
+#include <map>
+#include <set>
+#include "gsl/gsl_vector.h"
+#include "gsl/gsl_matrix.h"
+
+using namespace std;
+
+
+
+class SNPINFO {
+public:
+	string chr;
+	string rs_number;
+	double cM;
+	long int base_position;
+	string a_minor;
+	string a_major;
+	size_t n_miss;
+	double missingness;
+	double maf;	
+};
+
+//results for lmm
+class SUMSTAT {
+public:
+	double beta;				//REML estimator for beta
+	double se;				//SE for beta  
+	double lambda_remle;		//REML estimator for lambda
+	double lambda_mle;		//MLE estimator for lambda
+	double p_wald;			//p value from a Wald test
+	double p_lrt;				//p value from a likelihood ratio test
+	double p_score;			//p value from a score test
+};
+
+//results for mvlmm
+class MPHSUMSTAT {
+public:
+	vector<double> v_beta;	//REML estimator for beta
+	double p_wald;			//p value from a Wald test
+	double p_lrt;				//p value from a likelihood ratio test
+	double p_score;			//p value from a score test
+	vector<double> v_Vg;	//estimator for Vg, right half
+	vector<double> v_Ve;	//estimator for Ve, right half
+	vector<double> v_Vbeta;	//estimator for Vbeta, right half
+};
+
+
+//hyper-parameters for bslmm
+class HYPBSLMM {
+public:
+	double h;
+	double pve;
+	double rho;
+	double pge;
+	double logp;
+	
+	size_t n_gamma;
+};
+
+
+
+
+class PARAM {
+public:	
+	// IO related parameters
+	bool mode_silence;
+	int a_mode;				//analysis mode, 1/2/3/4 for Frequentist tests
+	int k_mode;				//kinship read mode: 1: n by n matrix, 2: id/id/k_value; 		
+	vector<size_t> p_column;			//which phenotype column needs analysis
+	size_t d_pace;		//display pace
+	
+	string file_bfile;
+	string file_geno;
+	string file_pheno;
+	string file_anno;		//optional
+	string file_cvt;		//optional
+	string file_kin;
+	string file_ku, file_kd;
+	string file_mk;
+	string file_out;
+	string path_out;
+	
+	string file_epm;		//estimated parameter file
+	string file_ebv;		//estimated breeding value file
+	string file_log;		//log file containing mean estimate
+	
+	string file_read;		//file containing total number of reads
+	string file_gene;		//gene expression file
+	
+	string file_snps;		//file containing analyzed snps or genes
+	
+	
+	
+	// QC related parameters	
+	double miss_level;
+	double maf_level;	
+	double hwe_level;
+	double r2_level;
+	
+	// LMM related parameters
+	double l_min;
+	double l_max;
+	size_t n_region;
+	double l_mle_null, l_remle_null;
+	double logl_mle_H0, logl_remle_H0;
+	double pve_null, pve_se_null;
+	double vg_remle_null, ve_remle_null, vg_mle_null, ve_mle_null;
+	vector<double> Vg_remle_null, Ve_remle_null, Vg_mle_null, Ve_mle_null;
+	vector<double> VVg_remle_null, VVe_remle_null, VVg_mle_null, VVe_mle_null;
+	vector<double> beta_remle_null, se_beta_remle_null, beta_mle_null, se_beta_mle_null;
+	double p_nr;	
+	double em_prec, nr_prec;
+	size_t em_iter, nr_iter;
+	size_t crt;
+	double pheno_mean;		//phenotype mean from bslmm fitting or for prediction
+
+	//for fitting multiple variance components
+	//the first three are of size n_vc, and the next two are of size n_vc+1
+	vector<double> v_traceG;
+	vector<double> v_pve;
+	vector<double> v_se_pve;
+
+	vector<double> v_sigma2;
+	vector<double> v_se_sigma2;	
+	vector<double> v_beta;
+	vector<double> v_se_beta;	
+	
+	// BSLMM MCMC related parameters
+	double h_min, h_max, h_scale;			//priors for h
+	double rho_min, rho_max, rho_scale;		//priors for rho
+	double logp_min, logp_max, logp_scale;		//priors for log(pi)
+	size_t s_min, s_max;			//minimum and maximum number of gammas
+	size_t w_step;					//number of warm up/burn in iterations
+	size_t s_step;					//number of sampling iterations
+	size_t r_pace;					//record pace
+	size_t w_pace;					//write pace
+	size_t n_accept;				//number of acceptance
+	size_t n_mh;					//number of MH steps within each iteration
+	double geo_mean;				//mean of the geometric distribution
+	long int randseed;
+	double trace_G;
+
+	HYPBSLMM cHyp_initial;
+		
+	// Summary statistics
+	bool error;
+	size_t ni_total, ni_test, ni_cvt;	//number of individuals
+	size_t np_obs, np_miss;		//number of observed and missing phenotypes
+	size_t ns_total, ns_test;	//number of snps
+	size_t ng_total, ng_test;	//number of genes
+	size_t ni_control, ni_case;	//number of controls and number of cases
+	size_t n_cvt;			//number of covariates
+	size_t n_ph;			//number of phenotypes
+	size_t n_vc;			//number of variance components (including the diagonal matrix)
+	double time_total;		//record total time
+	double time_G;			//time spent on reading files the second time and calculate K
+	double time_eigen;		//time spent on eigen-decomposition
+	double time_UtX;		//time spent on calculating UX and Uy
+	double time_UtZ;		//time spent on calculating UtZ, for probit BSLMM
+	double time_opt;		//time spent on optimization iterations/or mcmc
+	double time_Omega;		//time spent on calculating Omega
+	double time_hyp;		//time spent on sampling hyper-parameters, in PMM
+	double time_Proposal;  //time spend on constructing the proposal distribution (i.e. the initial lmm or lm analysis)
+
+	// Data
+	vector<vector<double> > pheno;			//a vector record all phenotypes, NA replaced with -9
+	vector<vector<double> > cvt;			//a vector record all covariates, NA replaced with -9	
+	vector<vector<int> > indicator_pheno;			//a matrix record when a phenotype is missing for an individual; 0 missing, 1 available
+	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<int> indicator_cvt;				//indicator for covariates, 0 missing, 1 available for analysis
+	
+	vector<int> indicator_bv;				//indicator for estimated breeding value file, 0 missing, 1 available for analysis
+	vector<int> indicator_read;				//indicator for read file, 0 missing, 1 available for analysis
+	vector<double> vec_read;				//total number of reads
+	vector<double> vec_bv;					//breeding values
+	vector<size_t> est_column;
+	
+	map<string, int> mapID2num;		//map small ID number to number, from 0 to n-1
+	map<string, string> mapRS2chr;		//map rs# to chromosome location
+	map<string, long int> mapRS2bp;		//map rs# to base position
+	map<string, double> mapRS2cM;		//map rs# to cM
+	map<string, double> mapRS2est;			//map rs# to parameters
+	
+	vector<SNPINFO> snpInfo;		//record SNP information
+	set<string> setSnps;			//a set of snps for analysis
+	
+	//constructor
+	PARAM();
+	
+	//functions
+	void ReadFiles ();		
+	void CheckParam (); 
+	void CheckData ();	
+	void PrintSummary ();
+	void ReadGenotypes (gsl_matrix *UtX, gsl_matrix *K, const bool calc_K);	
+	void CheckCvt ();
+	void CopyCvt (gsl_matrix *W);
+	void ProcessCvtPhen();
+	void CopyCvtPhen (gsl_matrix *W, gsl_vector *y, size_t flag);
+	void CopyCvtPhen (gsl_matrix *W, gsl_matrix *Y, size_t flag);
+	void CalcKin (gsl_matrix *matrix_kin);
+	void WriteMatrix (const gsl_matrix *matrix_U, const string suffix);
+	void WriteVector (const gsl_vector *vector_D, const string suffix);
+	void CopyRead (gsl_vector *log_N);
+};
+
+
+#endif
+