diff options
Diffstat (limited to 'src/mvlmm.h')
| -rw-r--r-- | src/mvlmm.h | 145 |
1 files changed, 71 insertions, 74 deletions
diff --git a/src/mvlmm.h b/src/mvlmm.h index d495c26..4329ad1 100644 --- a/src/mvlmm.h +++ b/src/mvlmm.h @@ -19,89 +19,86 @@ #ifndef __MVLMM_H__ #define __MVLMM_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; class MVLMM { 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_oxford; - string file_out; - string path_out; - - // MVLMM-related parameters. - double l_min; - double l_max; - size_t n_region; - double logl_remle_H0, logl_mle_H0; - 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; - vector<double> VVe_mle_null; - vector<double> beta_remle_null, se_beta_remle_null, beta_mle_null; - vector<double> se_beta_mle_null; - double p_nr; - size_t em_iter, nr_iter; - double em_prec, nr_prec; - size_t crt; - - // Summary statistics. - size_t ni_total, ni_test; // Number of individuals. - size_t ns_total, ns_test; // Number of SNPs. - size_t n_cvt; - size_t n_ph; - 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<MPHSUMSTAT> sumStat; // Output SNPSummary Data. - - // Main functions - void CopyFromParam (PARAM &cPar); - void CopyToParam (PARAM &cPar); - void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, - const gsl_matrix *UtW, const gsl_matrix *UtY); - void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, - const gsl_matrix *UtW, const gsl_matrix *UtY); - void Analyzebgen (const gsl_matrix *U, const gsl_vector *eval, - const gsl_matrix *UtW, const gsl_matrix *UtY); - void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval, - const gsl_matrix *UtW, const gsl_matrix *UtY, - const gsl_vector *env); - void AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval, - const gsl_matrix *UtW, const gsl_matrix *UtY, - const gsl_vector *env); - void WriteFiles (); - + // 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_oxford; + string file_out; + string path_out; + + // MVLMM-related parameters. + double l_min; + double l_max; + size_t n_region; + double logl_remle_H0, logl_mle_H0; + 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; + vector<double> VVe_mle_null; + vector<double> beta_remle_null, se_beta_remle_null, beta_mle_null; + vector<double> se_beta_mle_null; + double p_nr; + size_t em_iter, nr_iter; + double em_prec, nr_prec; + size_t crt; + + // Summary statistics. + size_t ni_total, ni_test; // Number of individuals. + size_t ns_total, ns_test; // Number of SNPs. + size_t n_cvt; + size_t n_ph; + 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<MPHSUMSTAT> sumStat; // Output SNPSummary Data. + + // Main functions + void CopyFromParam(PARAM &cPar); + void CopyToParam(PARAM &cPar); + void AnalyzeBimbam(const gsl_matrix *U, const gsl_vector *eval, + const gsl_matrix *UtW, const gsl_matrix *UtY); + void AnalyzePlink(const gsl_matrix *U, const gsl_vector *eval, + const gsl_matrix *UtW, const gsl_matrix *UtY); + void Analyzebgen(const gsl_matrix *U, const gsl_vector *eval, + const gsl_matrix *UtW, const gsl_matrix *UtY); + void AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval, + const gsl_matrix *UtW, const gsl_matrix *UtY, + const gsl_vector *env); + void AnalyzePlinkGXE(const gsl_matrix *U, const gsl_vector *eval, + const gsl_matrix *UtW, const gsl_matrix *UtY, + const gsl_vector *env); + void WriteFiles(); }; -void CalcMvLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, - const gsl_matrix *UtY, const size_t em_iter, - const size_t nr_iter, const double em_prec, - const double nr_prec, const double l_min, - const double l_max, const size_t n_region, - gsl_matrix *V_g, gsl_matrix *V_e, gsl_matrix *B, - gsl_matrix *se_B); +void CalcMvLmmVgVeBeta(const gsl_vector *eval, const gsl_matrix *UtW, + const gsl_matrix *UtY, const size_t em_iter, + const size_t nr_iter, const double em_prec, + const double nr_prec, const double l_min, + const double l_max, const size_t n_region, + gsl_matrix *V_g, gsl_matrix *V_e, gsl_matrix *B, + gsl_matrix *se_B); #endif - - |