diff options
Diffstat (limited to 'src/bslmm.h')
| -rw-r--r-- | src/bslmm.h | 48 |
1 files changed, 24 insertions, 24 deletions
diff --git a/src/bslmm.h b/src/bslmm.h index da185fa..c7768a2 100644 --- a/src/bslmm.h +++ b/src/bslmm.h @@ -1,22 +1,22 @@ /* 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 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 __BSLMM_H__ +#ifndef __BSLMM_H__ #define __BSLMM_H__ #include <vector> @@ -30,23 +30,23 @@ using namespace std; class BSLMM { -public: +public: // IO-related parameters. - int a_mode; + int a_mode; size_t d_pace; - + string file_bfile; string file_geno; string file_out; string path_out; - + // LMM-related parameters. double l_min; double l_max; size_t n_region; double pve_null; double pheno_mean; - + // BSLMM MCMC-related parameters double h_min, h_max, h_scale; // Priors for h. double rho_min, rho_max, rho_scale; // Priors for rho. @@ -61,8 +61,8 @@ public: size_t n_mh; // Number of MH steps per iter. double geo_mean; // Mean of geometric dist. long int randseed; - double trace_G; - + double trace_G; + HYPBSLMM cHyp_initial; // Summary statistics. @@ -74,32 +74,32 @@ public: // Time spent on constructing the proposal distribution for // gamma (i.e. lmm or lm analysis). - double time_Proposal; + double time_Proposal; // Indicator for individuals (phenotypes): 0 missing, 1 // available for analysis. - vector<int> indicator_idv; + 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<int> indicator_snp; // Record SNP information. - vector<SNPINFO> snpInfo; - + vector<SNPINFO> snpInfo; + // Not included in PARAM. - gsl_rng *gsl_r; - gsl_ran_discrete_t *gsl_t; - map<size_t, size_t> mapRank2pos; - + gsl_rng *gsl_r; + gsl_ran_discrete_t *gsl_t; + map<size_t, size_t> mapRank2pos; + // Main functions. void CopyFromParam (PARAM &cPar); void CopyToParam (PARAM &cPar); - + void RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *eval, const double lambda); - + void MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const gsl_vector *y); @@ -111,10 +111,10 @@ public: void WriteParam (const gsl_vector *alpha); void WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl_matrix *Result_gamma, const size_t w_col); - + // Subfunctions inside MCMC. void CalcPgamma (double *p_gammar); - + double CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const double sigma_a2); void InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, |