diff options
Diffstat (limited to 'src/param.h')
| -rw-r--r-- | src/param.h | 42 |
1 files changed, 27 insertions, 15 deletions
diff --git a/src/param.h b/src/param.h index 3c3b42e..4b4ad29 100644 --- a/src/param.h +++ b/src/param.h @@ -102,6 +102,8 @@ public: size_t n_col; size_t nmis_col; size_t nobs_col; + size_t ncase_col; + size_t ncontrol_col; size_t af_col; size_t var_col; size_t ws_col; @@ -120,23 +122,21 @@ public: vector<size_t> p_column; //which phenotype column needs analysis size_t d_pace; //display pace - string file_bfile; - string file_geno; + string file_bfile, file_mbfile; + string file_geno, file_mgeno; string file_pheno; string file_anno; //optional string file_gxe; //optional string file_cvt; //optional - string file_cat; + string file_cat, file_mcat; string file_var; string file_beta; string file_cor; - string file_kin; + string file_kin, file_mk; string file_ku, file_kd; - string file_mk; - string file_q, file_mq; - string file_s, file_ms; - string file_v, file_mv; - string file_weight; + string file_study, file_mstudy; + string file_ref, file_mref; + string file_weight, file_wsnp, file_wcat; string file_out; string path_out; @@ -165,7 +165,7 @@ public: 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 pve_null, pve_se_null, pve_total, se_pve_total; 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; @@ -185,6 +185,8 @@ public: vector<double> v_sigma2; vector<double> v_se_sigma2; + vector<double> v_enrich; + vector<double> v_se_enrich; vector<double> v_beta; vector<double> v_se_beta; @@ -210,15 +212,18 @@ public: size_t window_bp; size_t window_ns; + //vc related parameters + size_t n_block; + // Summary statistics bool error; - size_t ni_total, ni_test, ni_cvt; //number of individuals + size_t ni_total, ni_test, ni_cvt, ni_study, ni_ref; //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 ns_total, ns_test, ns_study, ns_ref; //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 ni_subsample; //number of subsampled individuals - size_t ni_total_ref, ns_total_ref, ns_pair;//max number of individuals, number of snps and number of snp pairs in the reference panel + //size_t ni_total_ref, ns_total_ref, ns_pair;//max number of individuals, number of snps and number of snp pairs in the reference panel 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) @@ -240,6 +245,7 @@ public: 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< vector<int> > mindicator_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_gxe; //indicator for gxe, 0 missing, 1 available for analysis vector<int> indicator_weight; //indicator for weight, 0 missing, 1 available for analysis @@ -256,9 +262,11 @@ public: map<string, double> mapRS2cM; //map rs# to cM map<string, double> mapRS2est; //map rs# to parameters map<string, size_t> mapRS2cat; //map rs# to category number - map<string, double> mapRS2var; //map rs# to category number + map<string, double> mapRS2wsnp; //map rs# to snp weights + map<string, vector<double> > mapRS2wcat; //map rs# to snp cat weights vector<SNPINFO> snpInfo; //record SNP information + vector< vector<SNPINFO> > msnpInfo; //record SNP information set<string> setSnps; //a set of snps for analysis //constructor @@ -279,12 +287,16 @@ public: 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 CalcS (gsl_matrix *S, gsl_matrix *Svar, gsl_matrix *Q); + void CalcS (const map<string, double> &mapRS2wA, const map<string, double> &mapRS2wK, const gsl_matrix *W, gsl_matrix *A, gsl_matrix *K, gsl_matrix *S, gsl_matrix *Svar, gsl_vector *ns); void WriteVector (const gsl_vector *q, const gsl_vector *s, const size_t n_total, const string suffix); void WriteVar (const string suffix); 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); + void ObtainWeight (const set<string> &setSnps_beta, map<string, double> &mapRS2wK); + void UpdateWeight (const size_t pve_flag, const map<string, double> &mapRS2wK, const size_t ni_test, const gsl_vector *ns, map<string, double> &mapRS2wA); + void UpdateSNPnZ (const map<string, double> &mapRS2wA, const map<string, string> &mapRS2A1, const map<string, double> &mapRS2z, gsl_vector *w, gsl_vector *z, vector<size_t> &vec_cat); + void UpdateSNP (const map<string, double> &mapRS2wA); }; |