diff options
Diffstat (limited to 'src/bslmmdap.h')
| -rw-r--r-- | src/bslmmdap.h | 62 |
1 files changed, 44 insertions, 18 deletions
diff --git a/src/bslmmdap.h b/src/bslmmdap.h index 7d95db7..8445669 100644 --- a/src/bslmmdap.h +++ b/src/bslmmdap.h @@ -50,39 +50,65 @@ public: 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 + 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 + 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<SNPINFO> snpInfo; //record SNP information + // Indicator for individuals (phenotypes): 0 missing, 1 + // available for analysis. + vector<int> indicator_idv; - // Main Functions + // 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. + + // 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); + 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 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); - +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 |