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Diffstat (limited to 'bslmm.cpp')
| -rw-r--r-- | bslmm.cpp | 1928 |
1 files changed, 0 insertions, 1928 deletions
diff --git a/bslmm.cpp b/bslmm.cpp deleted file mode 100644 index 55a05ca..0000000 --- a/bslmm.cpp +++ /dev/null @@ -1,1928 +0,0 @@ -/* - 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/>. - */ - -#include <iostream> -#include <fstream> -#include <sstream> - -#include <iomanip> -#include <cmath> -#include <iostream> -#include <stdio.h> -#include <stdlib.h> -#include <ctime> -#include <cstring> -#include <algorithm> - -#include "gsl/gsl_vector.h" -#include "gsl/gsl_matrix.h" -#include "gsl/gsl_linalg.h" -#include "gsl/gsl_blas.h" -#include "gsl/gsl_eigen.h" -#include "gsl/gsl_randist.h" -#include "gsl/gsl_cdf.h" -#include "gsl/gsl_roots.h" - - - - -#include "lapack.h" - -#ifdef FORCE_FLOAT -#include "param_float.h" -#include "bslmm_float.h" -#include "lmm_float.h" //for class FUNC_PARAM and MatrixCalcLR -#include "lm_float.h" -#include "mathfunc_float.h" //for function CenterVector -#else -#include "param.h" -#include "bslmm.h" -#include "lmm.h" -#include "lm.h" -#include "mathfunc.h" -#endif - -using namespace std; - - - - -void BSLMM::CopyFromParam (PARAM &cPar) -{ - a_mode=cPar.a_mode; - d_pace=cPar.d_pace; - - file_bfile=cPar.file_bfile; - file_geno=cPar.file_geno; - file_out=cPar.file_out; - path_out=cPar.path_out; - - l_min=cPar.h_min; - l_max=cPar.h_max; - n_region=cPar.n_region; - pve_null=cPar.pve_null; - pheno_mean=cPar.pheno_mean; - - time_UtZ=0.0; - time_Omega=0.0; - n_accept=0; - - h_min=cPar.h_min; - h_max=cPar.h_max; - h_scale=cPar.h_scale; - rho_min=cPar.rho_min; - rho_max=cPar.rho_max; - rho_scale=cPar.rho_scale; - logp_min=cPar.logp_min; - logp_max=cPar.logp_max; - logp_scale=cPar.logp_scale; - - s_min=cPar.s_min; - s_max=cPar.s_max; - w_step=cPar.w_step; - s_step=cPar.s_step; - r_pace=cPar.r_pace; - w_pace=cPar.w_pace; - n_mh=cPar.n_mh; - geo_mean=cPar.geo_mean; - randseed=cPar.randseed; - trace_G=cPar.trace_G; - - ni_total=cPar.ni_total; - ns_total=cPar.ns_total; - ni_test=cPar.ni_test; - ns_test=cPar.ns_test; - n_cvt=cPar.n_cvt; - - indicator_idv=cPar.indicator_idv; - indicator_snp=cPar.indicator_snp; - snpInfo=cPar.snpInfo; - - return; -} - - -void BSLMM::CopyToParam (PARAM &cPar) -{ - cPar.time_UtZ=time_UtZ; - cPar.time_Omega=time_Omega; - cPar.time_Proposal=time_Proposal; - cPar.cHyp_initial=cHyp_initial; - cPar.n_accept=n_accept; - cPar.pheno_mean=pheno_mean; - cPar.randseed=randseed; - - return; -} - - - -void BSLMM::WriteBV (const gsl_vector *bv) -{ - string file_str; - file_str=path_out+"/"+file_out; - file_str+=".bv.txt"; - - ofstream outfile (file_str.c_str(), ofstream::out); - if (!outfile) {cout<<"error writing file: "<<file_str.c_str()<<endl; return;} - - size_t t=0; - for (size_t i=0; i<ni_total; ++i) { - if (indicator_idv[i]==0) { - outfile<<"NA"<<endl; - } - else { - outfile<<scientific<<setprecision(6)<<gsl_vector_get(bv, t)<<endl; - t++; - } - } - - outfile.clear(); - outfile.close(); - return; -} - - - - -void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector *alpha, const size_t w) -{ - string file_str; - file_str=path_out+"/"+file_out; - file_str+=".param.txt"; - - ofstream outfile (file_str.c_str(), ofstream::out); - if (!outfile) {cout<<"error writing file: "<<file_str.c_str()<<endl; return;} - - outfile<<"chr"<<"\t"<<"rs"<<"\t" - <<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t" - <<"beta"<<"\t"<<"gamma"<<endl; - - size_t t=0; - for (size_t i=0; i<ns_total; ++i) { - if (indicator_snp[i]==0) {continue;} - - outfile<<snpInfo[i].chr<<"\t"<<snpInfo[i].rs_number<<"\t" - <<snpInfo[i].base_position<<"\t"<<snpInfo[i].n_miss<<"\t"; - - outfile<<scientific<<setprecision(6)<<gsl_vector_get(alpha, t)<<"\t"; - if (beta_g[t].second!=0) { - outfile<<beta_g[t].first/beta_g[t].second<<"\t"<<beta_g[t].second/(double)w<<endl; - } - else { - outfile<<0.0<<"\t"<<0.0<<endl; - } - t++; - } - - outfile.clear(); - outfile.close(); - return; -} - - -void BSLMM::WriteParam (const gsl_vector *alpha) -{ - string file_str; - file_str=path_out+"/"+file_out; - file_str+=".param.txt"; - - ofstream outfile (file_str.c_str(), ofstream::out); - if (!outfile) {cout<<"error writing file: "<<file_str.c_str()<<endl; return;} - - outfile<<"chr"<<"\t"<<"rs"<<"\t" - <<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t" - <<"beta"<<"\t"<<"gamma"<<endl; - - size_t t=0; - for (size_t i=0; i<ns_total; ++i) { - if (indicator_snp[i]==0) {continue;} - - outfile<<snpInfo[i].chr<<"\t"<<snpInfo[i].rs_number<<"\t" - <<snpInfo[i].base_position<<"\t"<<snpInfo[i].n_miss<<"\t"; - outfile<<scientific<<setprecision(6)<<gsl_vector_get(alpha, t)<<"\t"; - outfile<<0.0<<"\t"<<0.0<<endl; - t++; - } - - outfile.clear(); - outfile.close(); - return; -} - - -void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl_matrix *Result_gamma, const size_t w_col) -{ - string file_gamma, file_hyp; - file_gamma=path_out+"/"+file_out; - file_gamma+=".gamma.txt"; - file_hyp=path_out+"/"+file_out; - file_hyp+=".hyp.txt"; - - ofstream outfile_gamma, outfile_hyp; - - if (flag==0) { - outfile_gamma.open (file_gamma.c_str(), ofstream::out); - outfile_hyp.open (file_hyp.c_str(), ofstream::out); - if (!outfile_gamma) {cout<<"error writing file: "<<file_gamma<<endl; return;} - if (!outfile_hyp) {cout<<"error writing file: "<<file_hyp<<endl; return;} - - outfile_hyp<<"h \t pve \t rho \t pge \t pi \t n_gamma"<<endl; - - for (size_t i=0; i<s_max; ++i) { - outfile_gamma<<"s"<<i<<"\t"; - } - outfile_gamma<<endl; - } - else { - outfile_gamma.open (file_gamma.c_str(), ofstream::app); - outfile_hyp.open (file_hyp.c_str(), ofstream::app); - if (!outfile_gamma) {cout<<"error writing file: "<<file_gamma<<endl; return;} - if (!outfile_hyp) {cout<<"error writing file: "<<file_hyp<<endl; return;} - - size_t w; - if (w_col==0) {w=w_pace;} - else {w=w_col;} - - for (size_t i=0; i<w; ++i) { - outfile_hyp<<scientific; - for (size_t j=0; j<4; ++j) { - outfile_hyp<<setprecision(6)<<gsl_matrix_get (Result_hyp, i, j)<<"\t"; - } - outfile_hyp<<setprecision(6)<<exp(gsl_matrix_get (Result_hyp, i, 4))<<"\t"; - outfile_hyp<<(int)gsl_matrix_get (Result_hyp, i, 5)<<"\t"; - outfile_hyp<<endl; - } - - for (size_t i=0; i<w; ++i) { - for (size_t j=0; j<s_max; ++j) { - outfile_gamma<<(int)gsl_matrix_get (Result_gamma, i, j)<<"\t"; - } - outfile_gamma<<endl; - } - - } - - outfile_hyp.close(); - outfile_hyp.clear(); - outfile_gamma.close(); - outfile_gamma.clear(); - return; -} - - - -void BSLMM::CalcPgamma (double *p_gamma) -{ - double p, s=0.0; - for (size_t i=0; i<ns_test; ++i) { - p=0.7*gsl_ran_geometric_pdf (i+1, 1.0/geo_mean)+0.3/(double)ns_test; - p_gamma[i]=p; - s+=p; - } - for (size_t i=0; i<ns_test; ++i) { - p=p_gamma[i]; - p_gamma[i]=p/s; - } - return; -} - - - -void BSLMM::SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X, vector<size_t> &rank) -{ - size_t pos; - for (size_t i=0; i<rank.size(); ++i) { - pos=mapRank2pos[rank[i]]; - gsl_vector_view Xgamma_col=gsl_matrix_column (Xgamma, i); - gsl_vector_const_view X_col=gsl_matrix_const_column (X, pos); - gsl_vector_memcpy (&Xgamma_col.vector, &X_col.vector); - } - - return; -} - - - -double BSLMM::CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const double sigma_a2) -{ - double pve, var_y; - - gsl_matrix *Omega=gsl_matrix_alloc (UtXgamma->size2, UtXgamma->size2); - gsl_vector *Xty=gsl_vector_alloc (UtXgamma->size2); - gsl_vector *OiXty=gsl_vector_alloc (UtXgamma->size2); - - gsl_matrix_set_identity (Omega); - gsl_matrix_scale (Omega, 1.0/sigma_a2); - -#ifdef WITH_LAPACK - lapack_dgemm ((char *)"T", (char *)"N", 1.0, UtXgamma, UtXgamma, 1.0, Omega); -#else - gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, UtXgamma, UtXgamma, 1.0, Omega); -#endif - gsl_blas_dgemv (CblasTrans, 1.0, UtXgamma, Uty, 0.0, Xty); - - CholeskySolve(Omega, Xty, OiXty); - - gsl_blas_ddot (Xty, OiXty, &pve); - gsl_blas_ddot (Uty, Uty, &var_y); - - pve/=var_y; - - gsl_matrix_free (Omega); - gsl_vector_free (Xty); - gsl_vector_free (OiXty); - - return pve; -} - - -void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, vector<size_t> &rank, class HYPBSLMM &cHyp, vector<pair<size_t, double> > &pos_loglr) -{ - double q_genome=gsl_cdf_chisq_Qinv(0.05/(double)ns_test, 1); - - cHyp.n_gamma=0; - for (size_t i=0; i<pos_loglr.size(); ++i) { - if (2.0*pos_loglr[i].second>q_genome) {cHyp.n_gamma++;} - } - if (cHyp.n_gamma<10) {cHyp.n_gamma=10;} - - if (cHyp.n_gamma>s_max) {cHyp.n_gamma=s_max;} - if (cHyp.n_gamma<s_min) {cHyp.n_gamma=s_min;} - - rank.clear(); - for (size_t i=0; i<cHyp.n_gamma; ++i) { - rank.push_back(i); - } - - cHyp.logp=log((double)cHyp.n_gamma/(double)ns_test); - cHyp.h=pve_null; - - if (cHyp.logp==0) {cHyp.logp=-0.000001;} - if (cHyp.h==0) {cHyp.h=0.1;} - - gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp.n_gamma); - SetXgamma (UtXgamma, UtX, rank); - double sigma_a2; - if (trace_G!=0) { - sigma_a2=cHyp.h*1.0/(trace_G*(1-cHyp.h)*exp(cHyp.logp)*(double)ns_test); - } else { - sigma_a2=cHyp.h*1.0/( (1-cHyp.h)*exp(cHyp.logp)*(double)ns_test); - } - if (sigma_a2==0) {sigma_a2=0.025;} - cHyp.rho=CalcPveLM (UtXgamma, Uty, sigma_a2)/cHyp.h; - gsl_matrix_free (UtXgamma); - - if (cHyp.rho>1.0) {cHyp.rho=1.0;} - - if (cHyp.h<h_min) {cHyp.h=h_min;} - if (cHyp.h>h_max) {cHyp.h=h_max;} - if (cHyp.rho<rho_min) {cHyp.rho=rho_min;} - if (cHyp.rho>rho_max) {cHyp.rho=rho_max;} - if (cHyp.logp<logp_min) {cHyp.logp=logp_min;} - if (cHyp.logp>logp_max) {cHyp.logp=logp_max;} - - -// if (fix_sigma>=0) { -// fix_sigma=cHyp.h; -// rho_max=1-cHyp.h; -// cHyp.rho=rho_max/2.0; -// } - - //Initial for grid sampling: -// cHyp.h=0.225; -// cHyp.rho=1.0; -// cHyp.logp=-4.835429; - - cout<<"initial value of h = "<<cHyp.h<<endl; - cout<<"initial value of rho = "<<cHyp.rho<<endl; - cout<<"initial value of pi = "<<exp(cHyp.logp)<<endl; - cout<<"initial value of |gamma| = "<<cHyp.n_gamma<<endl; - - return; -} - - - -double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gsl_vector *Utu, gsl_vector *alpha_prime, class HYPBSLMM &cHyp) -{ - double sigma_b2=cHyp.h*(1.0-cHyp.rho)/(trace_G*(1-cHyp.h)); - - gsl_vector *Utu_rand=gsl_vector_alloc (Uty->size); - gsl_vector *weight_Hi=gsl_vector_alloc (Uty->size); - - double logpost=0.0; - double d, ds, uy, Hi_yy=0, logdet_H=0.0; - for (size_t i=0; i<ni_test; ++i) { - d=gsl_vector_get (K_eval, i)*sigma_b2; - ds=d/(d+1.0); - d=1.0/(d+1.0); - gsl_vector_set (weight_Hi, i, d); - - logdet_H-=log(d); - uy=gsl_vector_get (Uty, i); - Hi_yy+=d*uy*uy; - - gsl_vector_set (Utu_rand, i, gsl_ran_gaussian(gsl_r, 1)*sqrt(ds)); - } - - //sample tau - double tau=1.0; - if (a_mode==11) {tau = gsl_ran_gamma (gsl_r, (double)ni_test/2.0, 2.0/Hi_yy); } - - //sample alpha - gsl_vector_memcpy (alpha_prime, Uty); - gsl_vector_mul (alpha_prime, weight_Hi); - gsl_vector_scale (alpha_prime, sigma_b2); - - //sample u - gsl_vector_memcpy (Utu, alpha_prime); - gsl_vector_mul (Utu, K_eval); - if (a_mode==11) {gsl_vector_scale (Utu_rand, sqrt(1.0/tau));} - gsl_vector_add (Utu, Utu_rand); - - //for quantitative traits, calculate pve and ppe - if (a_mode==11) { - gsl_blas_ddot (Utu, Utu, &d); - cHyp.pve=d/(double)ni_test; - cHyp.pve/=cHyp.pve+1.0/tau; - cHyp.pge=0.0; - } - - //calculate likelihood - logpost=-0.5*logdet_H; - if (a_mode==11) {logpost-=0.5*(double)ni_test*log(Hi_yy);} - else {logpost-=0.5*Hi_yy;} - - logpost+=((double)cHyp.n_gamma-1.0)*cHyp.logp+((double)ns_test-(double)cHyp.n_gamma)*log(1-exp(cHyp.logp)); - - gsl_vector_free (Utu_rand); - gsl_vector_free (weight_Hi); - - return logpost; -} - - -double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const gsl_vector *K_eval, gsl_vector *UtXb, gsl_vector *Utu, gsl_vector *alpha_prime, gsl_vector *beta, class HYPBSLMM &cHyp) -{ - clock_t time_start; - - double sigma_a2=cHyp.h*cHyp.rho/(trace_G*(1-cHyp.h)*exp(cHyp.logp)*(double)ns_test); - double sigma_b2=cHyp.h*(1.0-cHyp.rho)/(trace_G*(1-cHyp.h)); - - double logpost=0.0; - double d, ds, uy, P_yy=0, logdet_O=0.0, logdet_H=0.0; - - gsl_matrix *UtXgamma_eval=gsl_matrix_alloc (UtXgamma->size1, UtXgamma->size2); - gsl_matrix *Omega=gsl_matrix_alloc (UtXgamma->size2, UtXgamma->size2); - gsl_vector *XtHiy=gsl_vector_alloc (UtXgamma->size2); - gsl_vector *beta_hat=gsl_vector_alloc (UtXgamma->size2); - gsl_vector *Utu_rand=gsl_vector_alloc (UtXgamma->size1); - gsl_vector *weight_Hi=gsl_vector_alloc (UtXgamma->size1); - - gsl_matrix_memcpy (UtXgamma_eval, UtXgamma); - - logdet_H=0.0; P_yy=0.0; - for (size_t i=0; i<ni_test; ++i) { - gsl_vector_view UtXgamma_row=gsl_matrix_row (UtXgamma_eval, i); - d=gsl_vector_get (K_eval, i)*sigma_b2; - ds=d/(d+1.0); - d=1.0/(d+1.0); - gsl_vector_set (weight_Hi, i, d); - - logdet_H-=log(d); - uy=gsl_vector_get (Uty, i); - P_yy+=d*uy*uy; - gsl_vector_scale (&UtXgamma_row.vector, d); - - gsl_vector_set (Utu_rand, i, gsl_ran_gaussian(gsl_r, 1)*sqrt(ds)); - } - - //calculate Omega - gsl_matrix_set_identity (Omega); - - time_start=clock(); -#ifdef WITH_LAPACK - lapack_dgemm ((char *)"T", (char *)"N", sigma_a2, UtXgamma_eval, UtXgamma, 1.0, Omega); -#else - gsl_blas_dgemm (CblasTrans, CblasNoTrans, sigma_a2, UtXgamma_eval, UtXgamma, 1.0, Omega); -#endif - time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - - - //calculate beta_hat - gsl_blas_dgemv (CblasTrans, 1.0, UtXgamma_eval, Uty, 0.0, XtHiy); - - logdet_O=CholeskySolve(Omega, XtHiy, beta_hat); - - gsl_vector_scale (beta_hat, sigma_a2); - - gsl_blas_ddot (XtHiy, beta_hat, &d); - P_yy-=d; - - //sample tau - double tau=1.0; - if (a_mode==11) {tau =gsl_ran_gamma (gsl_r, (double)ni_test/2.0, 2.0/P_yy); } - - //sample beta - for (size_t i=0; i<beta->size; i++) - { - d=gsl_ran_gaussian(gsl_r, 1); - gsl_vector_set(beta, i, d); - } - gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega, beta); - - - //it compuates inv(L^T(Omega)) %*% beta; - gsl_vector_scale(beta, sqrt(sigma_a2/tau)); - gsl_vector_add(beta, beta_hat); - gsl_blas_dgemv (CblasNoTrans, 1.0, UtXgamma, beta, 0.0, UtXb); - - //sample alpha - gsl_vector_memcpy (alpha_prime, Uty); - gsl_vector_sub (alpha_prime, UtXb); - gsl_vector_mul (alpha_prime, weight_Hi); - gsl_vector_scale (alpha_prime, sigma_b2); - - //sample u - gsl_vector_memcpy (Utu, alpha_prime); - gsl_vector_mul (Utu, K_eval); - - if (a_mode==11) {gsl_vector_scale (Utu_rand, sqrt(1.0/tau));} - gsl_vector_add (Utu, Utu_rand); - - - //for quantitative traits, calculate pve and pge - if (a_mode==11) { - gsl_blas_ddot (UtXb, UtXb, &d); - cHyp.pge=d/(double)ni_test; - - gsl_blas_ddot (Utu, Utu, &d); - cHyp.pve=cHyp.pge+d/(double)ni_test; - - if (cHyp.pve==0) {cHyp.pge=0.0;} - else {cHyp.pge/=cHyp.pve;} - cHyp.pve/=cHyp.pve+1.0/tau; - } - - - gsl_matrix_free (UtXgamma_eval); - gsl_matrix_free (Omega); - gsl_vector_free (XtHiy); - gsl_vector_free (beta_hat); - gsl_vector_free (Utu_rand); - gsl_vector_free (weight_Hi); - - logpost=-0.5*logdet_H-0.5*logdet_O; - if (a_mode==11) {logpost-=0.5*(double)ni_test*log(P_yy);} - else {logpost-=0.5*P_yy;} -// else {logpost+=-0.5*P_yy*tau+0.5*(double)ni_test*log(tau);} - logpost+=((double)cHyp.n_gamma-1.0)*cHyp.logp+((double)ns_test-(double)cHyp.n_gamma)*log(1.0-exp(cHyp.logp)); - - return logpost; -} - - - -//calculate pve and pge, and calculate z_hat for case-control data -void BSLMM::CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *Utu, gsl_vector *z_hat, class HYPBSLMM &cHyp) -{ - double d; - - gsl_blas_ddot (Utu, Utu, &d); - cHyp.pve=d/(double)ni_test; - - gsl_blas_dgemv (CblasNoTrans, 1.0, U, Utu, 0.0, z_hat); - - cHyp.pve/=cHyp.pve+1.0; - cHyp.pge=0.0; - - return; -} - - -//calculate pve and pge, and calculate z_hat for case-control data -void BSLMM::CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *UtXb, const gsl_vector *Utu, gsl_vector *z_hat, class HYPBSLMM &cHyp) -{ - double d; - gsl_vector *UtXbU=gsl_vector_alloc (Utu->size); - - gsl_blas_ddot (UtXb, UtXb, &d); - cHyp.pge=d/(double)ni_test; - - gsl_blas_ddot (Utu, Utu, &d); - cHyp.pve=cHyp.pge+d/(double)ni_test; - - gsl_vector_memcpy (UtXbU, Utu); - gsl_vector_add (UtXbU, UtXb); - gsl_blas_dgemv (CblasNoTrans, 1.0, U, UtXbU, 0.0, z_hat); - - if (cHyp.pve==0) {cHyp.pge=0.0;} - else {cHyp.pge/=cHyp.pve;} - - cHyp.pve/=cHyp.pve+1.0; - - gsl_vector_free(UtXbU); - return; -} - - - - -void BSLMM::SampleZ (const gsl_vector *y, const gsl_vector *z_hat, gsl_vector *z) -{ - double d1, d2, z_rand=0.0; - for (size_t i=0; i<z->size; ++i) { - d1=gsl_vector_get (y, i); - d2=gsl_vector_get (z_hat, i); - //y is centerred for case control studies - if (d1<=0.0) { - //control, right truncated - do { - z_rand=d2+gsl_ran_gaussian(gsl_r, 1.0); - } while (z_rand>0.0); - } - else { - do { - z_rand=d2+gsl_ran_gaussian(gsl_r, 1.0); - } while (z_rand<0.0); - } - - gsl_vector_set (z, i, z_rand); - } - - return; -} - - - - - -double BSLMM::ProposeHnRho (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat) -{ - - double h=cHyp_old.h, rho=cHyp_old.rho; - - double d_h=(h_max-h_min)*h_scale, d_rho=(rho_max-rho_min)*rho_scale; - - for (size_t i=0; i<repeat; ++i) { - h=h+(gsl_rng_uniform(gsl_r)-0.5)*d_h; - if (h<h_min) {h=2*h_min-h;} - if (h>h_max) {h=2*h_max-h;} - - rho=rho+(gsl_rng_uniform(gsl_r)-0.5)*d_rho; - if (rho<rho_min) {rho=2*rho_min-rho;} - if (rho>rho_max) {rho=2*rho_max-rho;} - } - /* - //Grid Sampling - for (size_t i=0; i<repeat; ++i) { - if (gsl_rng_uniform(gsl_r)<0.66) {continue;} - h=h+(gsl_rng_uniform_int(gsl_r, 2)-0.5)*0.1; - if (h<h_min) {h=h_max;} - if (h>h_max) {h=h_min;} - } - - for (size_t i=0; i<repeat; ++i) { - if (gsl_rng_uniform(gsl_r)<0.66) {continue;} - rho=rho+(gsl_rng_uniform_int(gsl_r, 2)-0.5)*0.1; - if (rho<rho_min) {rho=rho_max;} - if (rho>rho_max) {rho=rho_min;} - } - */ - cHyp_new.h=h; - cHyp_new.rho=rho; - return 0.0; -} - - -double BSLMM::ProposePi (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat) -{ - double logp_old=cHyp_old.logp, logp_new=cHyp_old.logp; - double log_ratio=0.0; - - double d_logp=min(0.1, (logp_max-logp_min)*logp_scale); - - for (size_t i=0; i<repeat; ++i) { - logp_new=logp_old+(gsl_rng_uniform(gsl_r)-0.5)*d_logp; - if (logp_new<logp_min) {logp_new=2*logp_min-logp_new;} - if (logp_new>logp_max) {logp_new=2*logp_max-logp_new;} - - log_ratio+=logp_new-logp_old; - logp_old=logp_new; - } - /* - //Grid Sampling - for (size_t i=0; i<repeat; ++i) { - if (gsl_rng_uniform(gsl_r)<0.66) {continue;} - logp_new=logp_old+(gsl_rng_uniform_int(gsl_r, 2)-0.5)*0.5*log(10.0); - if (logp_new<logp_min) {logp_new=logp_max;} - if (logp_new>logp_max) {logp_new=logp_min;} - - log_ratio+=logp_new-logp_old; - logp_old=logp_new; - } - */ - cHyp_new.logp=logp_new; - - return log_ratio; -} - -bool comp_vec (size_t a, size_t b) -{ - return (a < b); -} - - -double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank_new, const double *p_gamma, const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat) -{ - map<size_t, int> mapRank2in; - size_t r; - double unif, logp=0.0; - int flag_gamma; - size_t r_add, r_remove, col_id; - - rank_new.clear(); - if (cHyp_old.n_gamma!=rank_old.size()) {cout<<"size wrong"<<endl;} - - if (cHyp_old.n_gamma!=0) { - for (size_t i=0; i<rank_old.size(); ++i) { - r=rank_old[i]; - rank_new.push_back(r); - mapRank2in[r]=1; - } - } - cHyp_new.n_gamma=cHyp_old.n_gamma; - - for (size_t i=0; i<repeat; ++i) { - unif=gsl_rng_uniform(gsl_r); - - if (unif < 0.40 && cHyp_new.n_gamma<s_max) {flag_gamma=1;} - else if (unif>=0.40 && unif < 0.80 && cHyp_new.n_gamma>s_min) {flag_gamma=2;} - else if (unif>=0.80 && cHyp_new.n_gamma>0 && cHyp_new.n_gamma<ns_test) {flag_gamma=3;} - else {flag_gamma=4;} - - if(flag_gamma==1) {//add a snp; - do { - r_add=gsl_ran_discrete (gsl_r, gsl_t); - } while (mapRank2in.count(r_add)!=0); - - double prob_total=1.0; - for (size_t i=0; i<cHyp_new.n_gamma; ++i) { - r=rank_new[i]; - prob_total-=p_gamma[r]; - } - - mapRank2in[r_add]=1; - rank_new.push_back(r_add); - cHyp_new.n_gamma++; - logp+=-log(p_gamma[r_add]/prob_total)-log((double)cHyp_new.n_gamma); - } - else if (flag_gamma==2) {//delete a snp; - col_id=gsl_rng_uniform_int(gsl_r, cHyp_new.n_gamma); - r_remove=rank_new[col_id]; - - double prob_total=1.0; - for (size_t i=0; i<cHyp_new.n_gamma; ++i) { - r=rank_new[i]; - prob_total-=p_gamma[r]; - } - prob_total+=p_gamma[r_remove]; - - mapRank2in.erase(r_remove); - rank_new.erase(rank_new.begin()+col_id); - logp+=log(p_gamma[r_remove]/prob_total)+log((double)cHyp_new.n_gamma); - cHyp_new.n_gamma--; - } - else if (flag_gamma==3) {//switch a snp; - col_id=gsl_rng_uniform_int(gsl_r, cHyp_new.n_gamma); - r_remove=rank_new[col_id]; - //careful with the proposal - do { - r_add=gsl_ran_discrete (gsl_r, gsl_t); - } while (mapRank2in.count(r_add)!=0); - - double prob_total=1.0; - for (size_t i=0; i<cHyp_new.n_gamma; ++i) { - r=rank_new[i]; - prob_total-=p_gamma[r]; - } - - logp+=log(p_gamma[r_remove]/(prob_total+p_gamma[r_remove]-p_gamma[r_add]) ); - logp-=log(p_gamma[r_add]/prob_total); - - mapRank2in.erase(r_remove); - mapRank2in[r_add]=1; - rank_new.erase(rank_new.begin()+col_id); - rank_new.push_back(r_add); - } - else {logp+=0;}//do not change - } - - stable_sort (rank_new.begin(), rank_new.end(), comp_vec); - - mapRank2in.clear(); - return logp; -} - - - - - - -bool comp_lr (pair<size_t, double> a, pair<size_t, double> b) -{ - return (a.second > b.second); -} - - - - - - - -//if a_mode==13 then Uty==y -void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const gsl_vector *y) { - clock_t time_start; - - class HYPBSLMM cHyp_old, cHyp_new; - - gsl_matrix *Result_hyp=gsl_matrix_alloc (w_pace, 6); - gsl_matrix *Result_gamma=gsl_matrix_alloc (w_pace, s_max); - - gsl_vector *alpha_prime=gsl_vector_alloc (ni_test); - gsl_vector *alpha_new=gsl_vector_alloc (ni_test); - gsl_vector *alpha_old=gsl_vector_alloc (ni_test); - gsl_vector *Utu=gsl_vector_alloc (ni_test); - gsl_vector *Utu_new=gsl_vector_alloc (ni_test); - gsl_vector *Utu_old=gsl_vector_alloc (ni_test); - - gsl_vector *UtXb_new=gsl_vector_alloc (ni_test); - gsl_vector *UtXb_old=gsl_vector_alloc (ni_test); - - gsl_vector *z_hat=gsl_vector_alloc (ni_test); - gsl_vector *z=gsl_vector_alloc (ni_test); - gsl_vector *Utz=gsl_vector_alloc (ni_test); - - gsl_vector_memcpy (Utz, Uty); - - double logPost_new, logPost_old; - double logMHratio; - double mean_z=0.0; - - gsl_matrix_set_zero (Result_gamma); - gsl_vector_set_zero (Utu); - gsl_vector_set_zero (alpha_prime); - if (a_mode==13) { - pheno_mean=0.0; - } - - vector<pair<double, double> > beta_g; - for (size_t i=0; i<ns_test; i++) { - beta_g.push_back(make_pair(0.0, 0.0)); - } - - vector<size_t> rank_new, rank_old; - vector<double> beta_new, beta_old; - - vector<pair<size_t, double> > pos_loglr; - - time_start=clock(); - MatrixCalcLR (U, UtX, Utz, K_eval, l_min, l_max, n_region, pos_loglr); - time_Proposal=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - - stable_sort (pos_loglr.begin(), pos_loglr.end(), comp_lr); - for (size_t i=0; i<ns_test; ++i) { - mapRank2pos[i]=pos_loglr[i].first; - } - - //calculate proposal distribution for gamma (unnormalized), and set up gsl_r and gsl_t - gsl_rng_env_setup(); - const gsl_rng_type * gslType; - gslType = gsl_rng_default; - if (randseed<0) - { - time_t rawtime; - time (&rawtime); - tm * ptm = gmtime (&rawtime); - - randseed = (unsigned) (ptm->tm_hour%24*3600+ptm->tm_min*60+ptm->tm_sec); - } - gsl_r = gsl_rng_alloc(gslType); - gsl_rng_set(gsl_r, randseed); - - double *p_gamma = new double[ns_test]; - CalcPgamma (p_gamma); - - gsl_t=gsl_ran_discrete_preproc (ns_test, p_gamma); - - //initial parameters - InitialMCMC (UtX, Utz, rank_old, cHyp_old, pos_loglr); -// if (fix_sigma>=0) { -// rho_max=1-fix_sigma; -// cHyp_old.h=fix_sigma/(1-cHyp_old.rho); -// } - - cHyp_initial=cHyp_old; - - if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) { - logPost_old=CalcPosterior(Utz, K_eval, Utu_old, alpha_old, cHyp_old); - - beta_old.clear(); - for (size_t i=0; i<cHyp_old.n_gamma; ++i) { - beta_old.push_back(0); - } - } - else { - gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp_old.n_gamma); - gsl_vector *beta=gsl_vector_alloc (cHyp_old.n_gamma); - SetXgamma (UtXgamma, UtX, rank_old); - logPost_old=CalcPosterior(UtXgamma, Utz, K_eval, UtXb_old, Utu_old, alpha_old, beta, cHyp_old); - - beta_old.clear(); - for (size_t i=0; i<beta->size; ++i) { - beta_old.push_back(gsl_vector_get(beta, i)); - } - gsl_matrix_free (UtXgamma); - gsl_vector_free (beta); - } - - //calculate centered z_hat, and pve - if (a_mode==13) { - time_start=clock(); - if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) { - CalcCC_PVEnZ (U, Utu_old, z_hat, cHyp_old); - } - else { - CalcCC_PVEnZ (U, UtXb_old, Utu_old, z_hat, cHyp_old); - } - time_UtZ+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - } - - //start MCMC - int accept; - size_t total_step=w_step+s_step; - size_t w=0, w_col, pos; - size_t repeat=0; - - for (size_t t=0; t<total_step; ++t) { - if (t%d_pace==0 || t==total_step-1) {ProgressBar ("Running MCMC ", t, total_step-1, (double)n_accept/(double)(t*n_mh+1));} -// if (t>10) {break;} - - if (a_mode==13) { - SampleZ (y, z_hat, z); - mean_z=CenterVector (z); - - time_start=clock(); - gsl_blas_dgemv (CblasTrans, 1.0, U, z, 0.0, Utz); - time_UtZ+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - - //First proposal - if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) { - logPost_old=CalcPosterior(Utz, K_eval, Utu_old, alpha_old, cHyp_old); - beta_old.clear(); - for (size_t i=0; i<cHyp_old.n_gamma; ++i) { - beta_old.push_back(0); - } - } - else { - gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp_old.n_gamma); - gsl_vector *beta=gsl_vector_alloc (cHyp_old.n_gamma); - SetXgamma (UtXgamma, UtX, rank_old); - logPost_old=CalcPosterior(UtXgamma, Utz, K_eval, UtXb_old, Utu_old, alpha_old, beta, cHyp_old); - - beta_old.clear(); - for (size_t i=0; i<beta->size; ++i) { - beta_old.push_back(gsl_vector_get(beta, i)); - } - gsl_matrix_free (UtXgamma); - gsl_vector_free (beta); - } - } - - //MH steps - for (size_t i=0; i<n_mh; ++i) { - if (gsl_rng_uniform(gsl_r)<0.33) {repeat = 1+gsl_rng_uniform_int(gsl_r, 20);} - else {repeat=1;} - - logMHratio=0.0; - logMHratio+=ProposeHnRho(cHyp_old, cHyp_new, repeat); - logMHratio+=ProposeGamma (rank_old, rank_new, p_gamma, cHyp_old, cHyp_new, repeat); - logMHratio+=ProposePi(cHyp_old, cHyp_new, repeat); - -// if (fix_sigma>=0) { -// cHyp_new.h=fix_sigma/(1-cHyp_new.rho); -// } - - if (cHyp_new.n_gamma==0 || cHyp_new.rho==0) { - logPost_new=CalcPosterior(Utz, K_eval, Utu_new, alpha_new, cHyp_new); - beta_new.clear(); - for (size_t i=0; i<cHyp_new.n_gamma; ++i) { - beta_new.push_back(0); - } - } - else { - gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp_new.n_gamma); - gsl_vector *beta=gsl_vector_alloc (cHyp_new.n_gamma); - SetXgamma (UtXgamma, UtX, rank_new); - logPost_new=CalcPosterior(UtXgamma, Utz, K_eval, UtXb_new, Utu_new, alpha_new, beta, cHyp_new); - beta_new.clear(); - for (size_t i=0; i<beta->size; ++i) { - beta_new.push_back(gsl_vector_get(beta, i)); - } - gsl_matrix_free (UtXgamma); - gsl_vector_free (beta); - } - - logMHratio+=logPost_new-logPost_old; - - if (logMHratio>0 || log(gsl_rng_uniform(gsl_r))<logMHratio) {accept=1; n_accept++;} - else {accept=0;} - - if (accept==1) { - logPost_old=logPost_new; - rank_old.clear(); beta_old.clear(); - if (rank_new.size()!=0) { - for (size_t i=0; i<rank_new.size(); ++i) { - rank_old.push_back(rank_new[i]); - beta_old.push_back(beta_new[i]); - } - } - cHyp_old=cHyp_new; - gsl_vector_memcpy (alpha_old, alpha_new); - gsl_vector_memcpy (UtXb_old, UtXb_new); - gsl_vector_memcpy (Utu_old, Utu_new); - } - else {cHyp_new=cHyp_old;} - } - - //calculate z_hat, and pve - if (a_mode==13) { - time_start=clock(); - if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) { - CalcCC_PVEnZ (U, Utu_old, z_hat, cHyp_old); - } - else { - CalcCC_PVEnZ (U, UtXb_old, Utu_old, z_hat, cHyp_old); - } - - //sample mu and update z hat - gsl_vector_sub (z, z_hat); - mean_z+=CenterVector(z); - mean_z+=gsl_ran_gaussian(gsl_r, sqrt(1.0/(double) ni_test) ); - - gsl_vector_add_constant (z_hat, mean_z); - - time_UtZ+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - } - - //Save data - if (t<w_step) {continue;} - else { - if (t%r_pace==0) { - w_col=w%w_pace; - if (w_col==0) { - if (w==0) {WriteResult (0, Result_hyp, Result_gamma, w_col);} - else { - WriteResult (1, Result_hyp, Result_gamma, w_col); - gsl_matrix_set_zero (Result_hyp); - gsl_matrix_set_zero (Result_gamma); - } - } - - gsl_matrix_set (Result_hyp, w_col, 0, cHyp_old.h); - gsl_matrix_set (Result_hyp, w_col, 1, cHyp_old.pve); - gsl_matrix_set (Result_hyp, w_col, 2, cHyp_old.rho); - gsl_matrix_set (Result_hyp, w_col, 3, cHyp_old.pge); - gsl_matrix_set (Result_hyp, w_col, 4, cHyp_old.logp); - gsl_matrix_set (Result_hyp, w_col, 5, cHyp_old.n_gamma); - - for (size_t i=0; i<cHyp_old.n_gamma; ++i) { - pos=mapRank2pos[rank_old[i]]+1; - - gsl_matrix_set (Result_gamma, w_col, i, pos); - - beta_g[pos-1].first+=beta_old[i]; - beta_g[pos-1].second+=1.0; - } - - gsl_vector_add (alpha_prime, alpha_old); - gsl_vector_add (Utu, Utu_old); - - if (a_mode==13) { - pheno_mean+=mean_z; - } - - w++; - - } - - } - } - cout<<endl; - - w_col=w%w_pace; - WriteResult (1, Result_hyp, Result_gamma, w_col); - - gsl_matrix_free(Result_hyp); - gsl_matrix_free(Result_gamma); - - gsl_vector_free(z_hat); - gsl_vector_free(z); - gsl_vector_free(Utz); - gsl_vector_free(UtXb_new); - gsl_vector_free(UtXb_old); - gsl_vector_free(alpha_new); - gsl_vector_free(alpha_old); - gsl_vector_free(Utu_new); - gsl_vector_free(Utu_old); - - gsl_vector_scale (alpha_prime, 1.0/(double)w); - gsl_vector_scale (Utu, 1.0/(double)w); - if (a_mode==13) { - pheno_mean/=(double)w; - } - - gsl_vector *alpha=gsl_vector_alloc (ns_test); - gsl_blas_dgemv (CblasTrans, 1.0/(double)ns_test, UtX, alpha_prime, 0.0, alpha); - WriteParam (beta_g, alpha, w); - gsl_vector_free(alpha); - - gsl_blas_dgemv (CblasNoTrans, 1.0, U, Utu, 0.0, alpha_prime); - WriteBV(alpha_prime); - - gsl_vector_free(alpha_prime); - gsl_vector_free(Utu); - - delete [] p_gamma; - beta_g.clear(); - - return; -} - - - -void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *eval, const double lambda) -{ - gsl_vector *beta=gsl_vector_alloc (UtX->size2); - gsl_vector *H_eval=gsl_vector_alloc (Uty->size); - gsl_vector *bv=gsl_vector_alloc (Uty->size); - - gsl_vector_memcpy (H_eval, eval); - gsl_vector_scale (H_eval, lambda); - gsl_vector_add_constant (H_eval, 1.0); - - gsl_vector_memcpy (bv, Uty); - gsl_vector_div (bv, H_eval); - - gsl_blas_dgemv (CblasTrans, lambda/(double)UtX->size2, UtX, bv, 0.0, beta); - gsl_vector_add_constant (H_eval, -1.0); - gsl_vector_mul (H_eval, bv); - gsl_blas_dgemv (CblasNoTrans, 1.0, U, H_eval, 0.0, bv); - - WriteParam (beta); - WriteBV(bv); - - gsl_vector_free (H_eval); - gsl_vector_free (beta); - gsl_vector_free (bv); - - return; -} - - - - - - - - - - - - - - - - - -//below fits MCMC for rho=1 -void BSLMM::CalcXtX (const gsl_matrix *X, const gsl_vector *y, const size_t s_size, gsl_matrix *XtX, gsl_vector *Xty) -{ - time_t time_start=clock(); - gsl_matrix_const_view X_sub=gsl_matrix_const_submatrix(X, 0, 0, X->size1, s_size); - gsl_matrix_view XtX_sub=gsl_matrix_submatrix(XtX, 0, 0, s_size, s_size); - gsl_vector_view Xty_sub=gsl_vector_subvector(Xty, 0, s_size); - -#ifdef WITH_LAPACK - lapack_dgemm ((char *)"T", (char *)"N", 1.0, &X_sub.matrix, &X_sub.matrix, 0.0, &XtX_sub.matrix); -#else - gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, &X_sub.matrix, &X_sub.matrix, 0.0, &XtX_sub.matrix); -#endif - gsl_blas_dgemv(CblasTrans, 1.0, &X_sub.matrix, y, 0.0, &Xty_sub.vector); - - time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - - return; -} - - -void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_matrix *XtX_old, const gsl_vector *Xty_old, const gsl_vector *y, const vector<size_t> &rank_old, const vector<size_t> &rank_new, gsl_matrix *X_new, gsl_matrix *XtX_new, gsl_vector *Xty_new) -{ - double d; - - //rank_old and rank_new are sorted already inside PorposeGamma - //calculate vectors rank_remove and rank_add - // size_t v_size=max(rank_old.size(), rank_new.size()); - //make sure that v_size is larger than repeat - size_t v_size=20; - vector<size_t> rank_remove(v_size), rank_add(v_size), rank_union(s_max+v_size); - vector<size_t>::iterator it; - - it=set_difference (rank_old.begin(), rank_old.end(), rank_new.begin(), rank_new.end(), rank_remove.begin()); - rank_remove.resize(it-rank_remove.begin()); - - it=set_difference (rank_new.begin(), rank_new.end(), rank_old.begin(), rank_old.end(), rank_add.begin()); - rank_add.resize(it-rank_add.begin()); - - it=set_union (rank_new.begin(), rank_new.end(), rank_old.begin(), rank_old.end(), rank_union.begin()); - rank_union.resize(it-rank_union.begin()); - - //map rank_remove and rank_add - map<size_t, int> mapRank2in_remove, mapRank2in_add; - for (size_t i=0; i<rank_remove.size(); i++) { - mapRank2in_remove[rank_remove[i]]=1; - } - for (size_t i=0; i<rank_add.size(); i++) { - mapRank2in_add[rank_add[i]]=1; - } - - //obtain the subset of matrix/vector - gsl_matrix_const_view Xold_sub=gsl_matrix_const_submatrix(X_old, 0, 0, X_old->size1, rank_old.size()); - gsl_matrix_const_view XtXold_sub=gsl_matrix_const_submatrix(XtX_old, 0, 0, rank_old.size(), rank_old.size()); - gsl_vector_const_view Xtyold_sub=gsl_vector_const_subvector(Xty_old, 0, rank_old.size()); - - gsl_matrix_view Xnew_sub=gsl_matrix_submatrix(X_new, 0, 0, X_new->size1, rank_new.size()); - gsl_matrix_view XtXnew_sub=gsl_matrix_submatrix(XtX_new, 0, 0, rank_new.size(), rank_new.size()); - gsl_vector_view Xtynew_sub=gsl_vector_subvector(Xty_new, 0, rank_new.size()); - - //get X_new and calculate XtX_new - /* - if (rank_remove.size()==0 && rank_add.size()==0) { - gsl_matrix_memcpy(&Xnew_sub.matrix, &Xold_sub.matrix); - gsl_matrix_memcpy(&XtXnew_sub.matrix, &XtXold_sub.matrix); - gsl_vector_memcpy(&Xtynew_sub.vector, &Xtyold_sub.vector); - } else { - gsl_matrix *X_temp=gsl_matrix_alloc(X_old->size1, rank_old.size()-rank_remove.size() ); - gsl_matrix *XtX_temp=gsl_matrix_alloc(X_temp->size2, X_temp->size2); - gsl_vector *Xty_temp=gsl_vector_alloc(X_temp->size2); - - if (rank_remove.size()==0) { - gsl_matrix_memcpy (X_temp, &Xold_sub.matrix); - gsl_matrix_memcpy (XtX_temp, &XtXold_sub.matrix); - gsl_vector_memcpy (Xty_temp, &Xtyold_sub.vector); - } else { - size_t i_temp=0, j_temp; - for (size_t i=0; i<rank_old.size(); i++) { - if (mapRank2in_remove.count(rank_old[i])!=0) {continue;} - gsl_vector_const_view Xold_col=gsl_matrix_const_column(X_old, i); - gsl_vector_view Xtemp_col=gsl_matrix_column(X_temp, i_temp); - gsl_vector_memcpy (&Xtemp_col.vector, &Xold_col.vector); - - d=gsl_vector_get (Xty_old, i); - gsl_vector_set (Xty_temp, i_temp, d); - - j_temp=i_temp; - for (size_t j=i; j<rank_old.size(); j++) { - if (mapRank2in_remove.count(rank_old[j])!=0) {continue;} - d=gsl_matrix_get (XtX_old, i, j); - gsl_matrix_set (XtX_temp, i_temp, j_temp, d); - if (i_temp!=j_temp) {gsl_matrix_set (XtX_temp, j_temp, i_temp, d);} - j_temp++; - } - i_temp++; - } - } - - if (rank_add.size()==0) { - gsl_matrix_memcpy (&Xnew_sub.matrix, X_temp); - gsl_matrix_memcpy (&XtXnew_sub.matrix, XtX_temp); - gsl_vector_memcpy (&Xtynew_sub.vector, Xty_temp); - } else { - gsl_matrix *X_add=gsl_matrix_alloc(X_old->size1, rank_add.size() ); - gsl_matrix *XtX_aa=gsl_matrix_alloc(X_add->size2, X_add->size2); - gsl_matrix *XtX_at=gsl_matrix_alloc(X_add->size2, X_temp->size2); - gsl_vector *Xty_add=gsl_vector_alloc(X_add->size2); - - //get X_add - SetXgamma (X_add, X, rank_add); - - //get t(X_add)X_add and t(X_add)X_temp - clock_t time_start=clock(); - - //somehow the lapack_dgemm does not work here - //#ifdef WITH_LAPACK - //lapack_dgemm ((char *)"T", (char *)"N", 1.0, X_add, X_add, 0.0, XtX_aa); - //lapack_dgemm ((char *)"T", (char *)"N", 1.0, X_add, X_temp, 0.0, XtX_at); - - //#else - gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, X_add, X_add, 0.0, XtX_aa); - gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, X_add, X_temp, 0.0, XtX_at); - //#endif - gsl_blas_dgemv(CblasTrans, 1.0, X_add, y, 0.0, Xty_add); - - time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - - //save to X_new, XtX_new and Xty_new - size_t i_temp=0, j_temp, i_flag=0, j_flag=0; - for (size_t i=0; i<rank_new.size(); i++) { - if (mapRank2in_add.count(rank_new[i])!=0) {i_flag=1;} else {i_flag=0;} - gsl_vector_view Xnew_col=gsl_matrix_column(X_new, i); - if (i_flag==1) { - gsl_vector_view Xcopy_col=gsl_matrix_column(X_add, i-i_temp); - gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector); - } else { - gsl_vector_view Xcopy_col=gsl_matrix_column(X_temp, i_temp); - gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector); - } - - if (i_flag==1) { - d=gsl_vector_get (Xty_add, i-i_temp); - } else { - d=gsl_vector_get (Xty_temp, i_temp); - } - gsl_vector_set (Xty_new, i, d); - - j_temp=i_temp; - for (size_t j=i; j<rank_new.size(); j++) { - if (mapRank2in_add.count(rank_new[j])!=0) {j_flag=1;} else {j_flag=0;} - - if (i_flag==1 && j_flag==1) { - d=gsl_matrix_get(XtX_aa, i-i_temp, j-j_temp); - } else if (i_flag==1) { - d=gsl_matrix_get(XtX_at, i-i_temp, j_temp); - } else if (j_flag==1) { - d=gsl_matrix_get(XtX_at, j-j_temp, i_temp); - } else { - d=gsl_matrix_get(XtX_temp, i_temp, j_temp); - } - - gsl_matrix_set (XtX_new, i, j, d); - if (i!=j) {gsl_matrix_set (XtX_new, j, i, d);} - - if (j_flag==0) {j_temp++;} - } - if (i_flag==0) {i_temp++;} - } - - gsl_matrix_free(X_add); - gsl_matrix_free(XtX_aa); - gsl_matrix_free(XtX_at); - gsl_vector_free(Xty_add); - } - - gsl_matrix_free(X_temp); - gsl_matrix_free(XtX_temp); - gsl_vector_free(Xty_temp); - } - */ - - - if (rank_remove.size()==0 && rank_add.size()==0) { - gsl_matrix_memcpy(&Xnew_sub.matrix, &Xold_sub.matrix); - gsl_matrix_memcpy(&XtXnew_sub.matrix, &XtXold_sub.matrix); - gsl_vector_memcpy(&Xtynew_sub.vector, &Xtyold_sub.vector); - } else { - size_t i_old, j_old, i_new, j_new, i_add, j_add, i_flag, j_flag; - if (rank_add.size()==0) { - i_old=0; i_new=0; - for (size_t i=0; i<rank_union.size(); i++) { - if (mapRank2in_remove.count(rank_old[i_old])!=0) {i_old++; continue;} - - gsl_vector_view Xnew_col=gsl_matrix_column(X_new, i_new); - gsl_vector_const_view Xcopy_col=gsl_matrix_const_column(X_old, i_old); - gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector); - - d=gsl_vector_get (Xty_old, i_old); - gsl_vector_set (Xty_new, i_new, d); - - j_old=i_old; j_new=i_new; - for (size_t j=i; j<rank_union.size(); j++) { - if (mapRank2in_remove.count(rank_old[j_old])!=0) {j_old++; continue;} - - d=gsl_matrix_get(XtX_old, i_old, j_old); - - gsl_matrix_set (XtX_new, i_new, j_new, d); - if (i_new!=j_new) {gsl_matrix_set (XtX_new, j_new, i_new, d);} - - j_old++; j_new++; - } - i_old++; i_new++; - } - } else { - gsl_matrix *X_add=gsl_matrix_alloc(X_old->size1, rank_add.size() ); - gsl_matrix *XtX_aa=gsl_matrix_alloc(X_add->size2, X_add->size2); - gsl_matrix *XtX_ao=gsl_matrix_alloc(X_add->size2, X_old->size2); - gsl_vector *Xty_add=gsl_vector_alloc(X_add->size2); - - //get X_add - SetXgamma (X_add, X, rank_add); - - //get t(X_add)X_add and t(X_add)X_temp - clock_t time_start=clock(); - - //somehow the lapack_dgemm does not work here - //#ifdef WITH_LAPACK - //lapack_dgemm ((char *)"T", (char *)"N", 1.0, X_add, X_add, 0.0, XtX_aa); - //lapack_dgemm ((char *)"T", (char *)"N", 1.0, X_add, X_temp, 0.0, XtX_at); - - //#else - gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, X_add, X_add, 0.0, XtX_aa); - gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, X_add, X_old, 0.0, XtX_ao); - //#endif - gsl_blas_dgemv(CblasTrans, 1.0, X_add, y, 0.0, Xty_add); - - time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - - //save to X_new, XtX_new and Xty_new - i_old=0; i_new=0; i_add=0; - for (size_t i=0; i<rank_union.size(); i++) { - if (mapRank2in_remove.count(rank_old[i_old])!=0) {i_old++; continue;} - if (mapRank2in_add.count(rank_new[i_new])!=0) {i_flag=1;} else {i_flag=0;} - - gsl_vector_view Xnew_col=gsl_matrix_column(X_new, i_new); - if (i_flag==1) { - gsl_vector_view Xcopy_col=gsl_matrix_column(X_add, i_add); - gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector); - } else { - gsl_vector_const_view Xcopy_col=gsl_matrix_const_column(X_old, i_old); - gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector); - } - - if (i_flag==1) { - d=gsl_vector_get (Xty_add, i_add); - } else { - d=gsl_vector_get (Xty_old, i_old); - } - gsl_vector_set (Xty_new, i_new, d); - - j_old=i_old; j_new=i_new; j_add=i_add; - for (size_t j=i; j<rank_union.size(); j++) { - if (mapRank2in_remove.count(rank_old[j_old])!=0) {j_old++; continue;} - if (mapRank2in_add.count(rank_new[j_new])!=0) {j_flag=1;} else {j_flag=0;} - - if (i_flag==1 && j_flag==1) { - d=gsl_matrix_get(XtX_aa, i_add, j_add); - } else if (i_flag==1) { - d=gsl_matrix_get(XtX_ao, i_add, j_old); - } else if (j_flag==1) { - d=gsl_matrix_get(XtX_ao, j_add, i_old); - } else { - d=gsl_matrix_get(XtX_old, i_old, j_old); - } - - gsl_matrix_set (XtX_new, i_new, j_new, d); - if (i_new!=j_new) {gsl_matrix_set (XtX_new, j_new, i_new, d);} - - j_new++; if (j_flag==1) {j_add++;} else {j_old++;} - } - i_new++; if (i_flag==1) {i_add++;} else {i_old++;} - } - - gsl_matrix_free(X_add); - gsl_matrix_free(XtX_aa); - gsl_matrix_free(XtX_ao); - gsl_vector_free(Xty_add); - } - - } - - rank_remove.clear(); - rank_add.clear(); - rank_union.clear(); - mapRank2in_remove.clear(); - mapRank2in_add.clear(); - - return; -} - - -double BSLMM::CalcPosterior (const double yty, class HYPBSLMM &cHyp) -{ - double logpost=0.0; - - //for quantitative traits, calculate pve and pge - //pve and pge for case/control data are calculted in CalcCC_PVEnZ - if (a_mode==11) { - cHyp.pve=0.0; - cHyp.pge=1.0; - } - - //calculate likelihood - if (a_mode==11) {logpost-=0.5*(double)ni_test*log(yty);} - else {logpost-=0.5*yty;} - - logpost+=((double)cHyp.n_gamma-1.0)*cHyp.logp+((double)ns_test-(double)cHyp.n_gamma)*log(1-exp(cHyp.logp)); - - return logpost; -} - - -double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX, const gsl_vector *Xty, const double yty, const size_t s_size, gsl_vector *Xb, gsl_vector *beta, class HYPBSLMM &cHyp) -{ - double sigma_a2=cHyp.h/( (1-cHyp.h)*exp(cHyp.logp)*(double)ns_test); - double logpost=0.0; - double d, P_yy=yty, logdet_O=0.0; - - gsl_matrix_const_view Xgamma_sub=gsl_matrix_const_submatrix (Xgamma, 0, 0, Xgamma->size1, s_size); - gsl_matrix_const_view XtX_sub=gsl_matrix_const_submatrix (XtX, 0, 0, s_size, s_size); - gsl_vector_const_view Xty_sub=gsl_vector_const_subvector (Xty, 0, s_size); - - gsl_matrix *Omega=gsl_matrix_alloc (s_size, s_size); - gsl_matrix *M_temp=gsl_matrix_alloc (s_size, s_size); - gsl_vector *beta_hat=gsl_vector_alloc (s_size); - gsl_vector *Xty_temp=gsl_vector_alloc (s_size); - - gsl_vector_memcpy (Xty_temp, &Xty_sub.vector); - - //calculate Omega - gsl_matrix_memcpy (Omega, &XtX_sub.matrix); - gsl_matrix_scale (Omega, sigma_a2); - gsl_matrix_set_identity (M_temp); - gsl_matrix_add (Omega, M_temp); - - //calculate beta_hat - logdet_O=CholeskySolve(Omega, Xty_temp, beta_hat); - gsl_vector_scale (beta_hat, sigma_a2); - - gsl_blas_ddot (Xty_temp, beta_hat, &d); - P_yy-=d; - - //sample tau - double tau=1.0; - if (a_mode==11) {tau =gsl_ran_gamma (gsl_r, (double)ni_test/2.0, 2.0/P_yy); } - - //sample beta - for (size_t i=0; i<s_size; i++) - { - d=gsl_ran_gaussian(gsl_r, 1); - gsl_vector_set(beta, i, d); - } - gsl_vector_view beta_sub=gsl_vector_subvector(beta, 0, s_size); - gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega, &beta_sub.vector); - - //it compuates inv(L^T(Omega)) %*% beta; - gsl_vector_scale(&beta_sub.vector, sqrt(sigma_a2/tau)); - gsl_vector_add(&beta_sub.vector, beta_hat); - gsl_blas_dgemv (CblasNoTrans, 1.0, &Xgamma_sub.matrix, &beta_sub.vector, 0.0, Xb); - - //for quantitative traits, calculate pve and pge - if (a_mode==11) { - gsl_blas_ddot (Xb, Xb, &d); - cHyp.pve=d/(double)ni_test; - cHyp.pve/=cHyp.pve+1.0/tau; - cHyp.pge=1.0; - } - - logpost=-0.5*logdet_O; - if (a_mode==11) {logpost-=0.5*(double)ni_test*log(P_yy);} - else {logpost-=0.5*P_yy;} - - logpost+=((double)cHyp.n_gamma-1.0)*cHyp.logp+((double)ns_test-(double)cHyp.n_gamma)*log(1.0-exp(cHyp.logp)); - - gsl_matrix_free (Omega); - gsl_matrix_free (M_temp); - gsl_vector_free (beta_hat); - gsl_vector_free (Xty_temp); - - return logpost; -} - - - -//calculate pve and pge, and calculate z_hat for case-control data -void BSLMM::CalcCC_PVEnZ (gsl_vector *z_hat, class HYPBSLMM &cHyp) -{ - gsl_vector_set_zero(z_hat); - cHyp.pve=0.0; - cHyp.pge=1.0; - return; -} - - -//calculate pve and pge, and calculate z_hat for case-control data -void BSLMM::CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat, class HYPBSLMM &cHyp) -{ - double d; - - gsl_blas_ddot (Xb, Xb, &d); - cHyp.pve=d/(double)ni_test; - cHyp.pve/=cHyp.pve+1.0; - cHyp.pge=1.0; - - gsl_vector_memcpy (z_hat, Xb); - - return; -} - - - -//if a_mode==13, then run probit model -void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) { - clock_t time_start; - double time_set=0, time_post=0; - - class HYPBSLMM cHyp_old, cHyp_new; - - gsl_matrix *Result_hyp=gsl_matrix_alloc (w_pace, 6); - gsl_matrix *Result_gamma=gsl_matrix_alloc (w_pace, s_max); - - gsl_vector *Xb_new=gsl_vector_alloc (ni_test); - gsl_vector *Xb_old=gsl_vector_alloc (ni_test); - gsl_vector *z_hat=gsl_vector_alloc (ni_test); - gsl_vector *z=gsl_vector_alloc (ni_test); - - gsl_matrix *Xgamma_old=gsl_matrix_alloc (ni_test, s_max); - gsl_matrix *XtX_old=gsl_matrix_alloc (s_max, s_max); - gsl_vector *Xtz_old=gsl_vector_alloc (s_max); - gsl_vector *beta_old=gsl_vector_alloc (s_max); - - gsl_matrix *Xgamma_new=gsl_matrix_alloc (ni_test, s_max); - gsl_matrix *XtX_new=gsl_matrix_alloc (s_max, s_max); - gsl_vector *Xtz_new=gsl_vector_alloc (s_max); - gsl_vector *beta_new=gsl_vector_alloc (s_max); - - double ztz=0.0; - gsl_vector_memcpy (z, y); - //for quantitative traits, y is centered already in gemma.cpp, but just in case - double mean_z=CenterVector (z); - gsl_blas_ddot(z, z, &ztz); - - double logPost_new, logPost_old; - double logMHratio; - - gsl_matrix_set_zero (Result_gamma); - if (a_mode==13) { - pheno_mean=0.0; - } - - vector<pair<double, double> > beta_g; - for (size_t i=0; i<ns_test; i++) { - beta_g.push_back(make_pair(0.0, 0.0)); - } - - vector<size_t> rank_new, rank_old; - vector<pair<size_t, double> > pos_loglr; - - time_start=clock(); - MatrixCalcLmLR (X, z, pos_loglr); - time_Proposal=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - - stable_sort (pos_loglr.begin(), pos_loglr.end(), comp_lr); - for (size_t i=0; i<ns_test; ++i) { - mapRank2pos[i]=pos_loglr[i].first; - } - - //calculate proposal distribution for gamma (unnormalized), and set up gsl_r and gsl_t - gsl_rng_env_setup(); - const gsl_rng_type * gslType; - gslType = gsl_rng_default; - if (randseed<0) - { - time_t rawtime; - time (&rawtime); - tm * ptm = gmtime (&rawtime); - - randseed = (unsigned) (ptm->tm_hour%24*3600+ptm->tm_min*60+ptm->tm_sec); - } - gsl_r = gsl_rng_alloc(gslType); - gsl_rng_set(gsl_r, randseed); - - double *p_gamma = new double[ns_test]; - CalcPgamma (p_gamma); - - gsl_t=gsl_ran_discrete_preproc (ns_test, p_gamma); - - //initial parameters - InitialMCMC (X, z, rank_old, cHyp_old, pos_loglr); - - cHyp_initial=cHyp_old; - - if (cHyp_old.n_gamma==0) { - logPost_old=CalcPosterior (ztz, cHyp_old); - } - else { - SetXgamma (Xgamma_old, X, rank_old); - CalcXtX (Xgamma_old, z, rank_old.size(), XtX_old, Xtz_old); - logPost_old=CalcPosterior (Xgamma_old, XtX_old, Xtz_old, ztz, rank_old.size(), Xb_old, beta_old, cHyp_old); - } - - //calculate centered z_hat, and pve - if (a_mode==13) { - if (cHyp_old.n_gamma==0) { - CalcCC_PVEnZ (z_hat, cHyp_old); - } - else { - CalcCC_PVEnZ (Xb_old, z_hat, cHyp_old); - } - } - - //start MCMC - int accept; - size_t total_step=w_step+s_step; - size_t w=0, w_col, pos; - size_t repeat=0; - - for (size_t t=0; t<total_step; ++t) { - if (t%d_pace==0 || t==total_step-1) {ProgressBar ("Running MCMC ", t, total_step-1, (double)n_accept/(double)(t*n_mh+1));} -// if (t>10) {break;} - if (a_mode==13) { - SampleZ (y, z_hat, z); - mean_z=CenterVector (z); - gsl_blas_ddot(z,z,&ztz); - - //First proposal - if (cHyp_old.n_gamma==0) { - logPost_old=CalcPosterior (ztz, cHyp_old); - } else { - gsl_matrix_view Xold_sub=gsl_matrix_submatrix(Xgamma_old, 0, 0, ni_test, rank_old.size()); - gsl_vector_view Xtz_sub=gsl_vector_subvector(Xtz_old, 0, rank_old.size()); - gsl_blas_dgemv (CblasTrans, 1.0, &Xold_sub.matrix, z, 0.0, &Xtz_sub.vector); - logPost_old=CalcPosterior (Xgamma_old, XtX_old, Xtz_old, ztz, rank_old.size(), Xb_old, beta_old, cHyp_old); - } - } - - //MH steps - for (size_t i=0; i<n_mh; ++i) { - if (gsl_rng_uniform(gsl_r)<0.33) {repeat = 1+gsl_rng_uniform_int(gsl_r, 20);} - else {repeat=1;} - - logMHratio=0.0; - logMHratio+=ProposeHnRho(cHyp_old, cHyp_new, repeat); - logMHratio+=ProposeGamma (rank_old, rank_new, p_gamma, cHyp_old, cHyp_new, repeat); - logMHratio+=ProposePi(cHyp_old, cHyp_new, repeat); - - if (cHyp_new.n_gamma==0) { - logPost_new=CalcPosterior (ztz, cHyp_new); - } else { - //this if makes sure that rank_old.size()==rank_remove.size() does not happen - if (cHyp_new.n_gamma<=20 || cHyp_old.n_gamma<=20) { - time_start=clock(); - SetXgamma (Xgamma_new, X, rank_new); - CalcXtX (Xgamma_new, z, rank_new.size(), XtX_new, Xtz_new); - time_set+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - } else { - time_start=clock(); - SetXgamma (X, Xgamma_old, XtX_old, Xtz_old, z, rank_old, rank_new, Xgamma_new, XtX_new, Xtz_new); - time_set+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - } - time_start=clock(); - logPost_new=CalcPosterior (Xgamma_new, XtX_new, Xtz_new, ztz, rank_new.size(), Xb_new, beta_new, cHyp_new); - time_post+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - } - logMHratio+=logPost_new-logPost_old; - - if (logMHratio>0 || log(gsl_rng_uniform(gsl_r))<logMHratio) {accept=1; n_accept++;} - else {accept=0;} - - //cout<<rank_new.size()<<"\t"<<rank_old.size()<<"\t"<<logPost_new<<"\t"<<logPost_old<<endl; - if (accept==1) { - logPost_old=logPost_new; - cHyp_old=cHyp_new; - gsl_vector_memcpy (Xb_old, Xb_new); - - rank_old.clear(); - if (rank_new.size()!=0) { - for (size_t i=0; i<rank_new.size(); ++i) { - rank_old.push_back(rank_new[i]); - } - - gsl_matrix_view Xold_sub=gsl_matrix_submatrix(Xgamma_old, 0, 0, ni_test, rank_new.size()); - gsl_matrix_view XtXold_sub=gsl_matrix_submatrix(XtX_old, 0, 0, rank_new.size(), rank_new.size()); - gsl_vector_view Xtzold_sub=gsl_vector_subvector(Xtz_old, 0, rank_new.size()); - gsl_vector_view betaold_sub=gsl_vector_subvector(beta_old, 0, rank_new.size()); - - gsl_matrix_view Xnew_sub=gsl_matrix_submatrix(Xgamma_new, 0, 0, ni_test, rank_new.size()); - gsl_matrix_view XtXnew_sub=gsl_matrix_submatrix(XtX_new, 0, 0, rank_new.size(), rank_new.size()); - gsl_vector_view Xtznew_sub=gsl_vector_subvector(Xtz_new, 0, rank_new.size()); - gsl_vector_view betanew_sub=gsl_vector_subvector(beta_new, 0, rank_new.size()); - - gsl_matrix_memcpy(&Xold_sub.matrix, &Xnew_sub.matrix); - gsl_matrix_memcpy(&XtXold_sub.matrix, &XtXnew_sub.matrix); - gsl_vector_memcpy(&Xtzold_sub.vector, &Xtznew_sub.vector); - gsl_vector_memcpy(&betaold_sub.vector, &betanew_sub.vector); - } - } else { - cHyp_new=cHyp_old; - } - - } - - //calculate z_hat, and pve - if (a_mode==13) { - if (cHyp_old.n_gamma==0) { - CalcCC_PVEnZ (z_hat, cHyp_old); - } - else { - CalcCC_PVEnZ (Xb_old, z_hat, cHyp_old); - } - - //sample mu and update z hat - gsl_vector_sub (z, z_hat); - mean_z+=CenterVector(z); - mean_z+=gsl_ran_gaussian(gsl_r, sqrt(1.0/(double) ni_test) ); - - gsl_vector_add_constant (z_hat, mean_z); - } - - //Save data - if (t<w_step) {continue;} - else { - if (t%r_pace==0) { - w_col=w%w_pace; - if (w_col==0) { - if (w==0) {WriteResult (0, Result_hyp, Result_gamma, w_col);} - else { - WriteResult (1, Result_hyp, Result_gamma, w_col); - gsl_matrix_set_zero (Result_hyp); - gsl_matrix_set_zero (Result_gamma); - } - } - - gsl_matrix_set (Result_hyp, w_col, 0, cHyp_old.h); - gsl_matrix_set (Result_hyp, w_col, 1, cHyp_old.pve); - gsl_matrix_set (Result_hyp, w_col, 2, cHyp_old.rho); - gsl_matrix_set (Result_hyp, w_col, 3, cHyp_old.pge); - gsl_matrix_set (Result_hyp, w_col, 4, cHyp_old.logp); - gsl_matrix_set (Result_hyp, w_col, 5, cHyp_old.n_gamma); - - for (size_t i=0; i<cHyp_old.n_gamma; ++i) { - pos=mapRank2pos[rank_old[i]]+1; - - gsl_matrix_set (Result_gamma, w_col, i, pos); - - beta_g[pos-1].first+=gsl_vector_get(beta_old, i); - beta_g[pos-1].second+=1.0; - } - - if (a_mode==13) { - pheno_mean+=mean_z; - } - - w++; - - } - - } - } - cout<<endl; - - cout<<"time on selecting Xgamma: "<<time_set<<endl; - cout<<"time on calculating posterior: "<<time_post<<endl; - - w_col=w%w_pace; - WriteResult (1, Result_hyp, Result_gamma, w_col); - - gsl_vector *alpha=gsl_vector_alloc (ns_test); - gsl_vector_set_zero (alpha); - WriteParam (beta_g, alpha, w); - gsl_vector_free(alpha); - - gsl_matrix_free(Result_hyp); - gsl_matrix_free(Result_gamma); - - gsl_vector_free(z_hat); - gsl_vector_free(z); - gsl_vector_free(Xb_new); - gsl_vector_free(Xb_old); - - gsl_matrix_free(Xgamma_old); - gsl_matrix_free(XtX_old); - gsl_vector_free(Xtz_old); - gsl_vector_free(beta_old); - - gsl_matrix_free(Xgamma_new); - gsl_matrix_free(XtX_new); - gsl_vector_free(Xtz_new); - gsl_vector_free(beta_new); - - delete [] p_gamma; - beta_g.clear(); - - return; -} |