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authorPeter Carbonetto2017-06-07 23:23:35 -0500
committerPeter Carbonetto2017-06-07 23:23:35 -0500
commit93a7a2adb03f61e80badf6a5004fa4850dbb7d48 (patch)
tree72eb62acf1bc21000cd969e62658261590eab36e /src
parent35e4ee4767c35c2436fea81788742641172ada37 (diff)
downloadpangemma-93a7a2adb03f61e80badf6a5004fa4850dbb7d48.tar.gz
Removed FORCE_FLOAT from a few more files.
Diffstat (limited to 'src')
-rw-r--r--src/bslmm.cpp839
-rw-r--r--src/bslmm.h158
-rw-r--r--src/bslmmdap.cpp260
-rw-r--r--src/bslmmdap.h62
-rw-r--r--src/gemma.h17
-rw-r--r--src/lmm.h113
-rw-r--r--src/logistic.cpp46
-rw-r--r--src/mvlmm.h81
8 files changed, 874 insertions, 702 deletions
diff --git a/src/bslmm.cpp b/src/bslmm.cpp
index d295fd8..92762e2 100644
--- a/src/bslmm.cpp
+++ b/src/bslmm.cpp
@@ -14,7 +14,7 @@
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>
@@ -47,8 +47,7 @@
using namespace std;
-void BSLMM::CopyFromParam (PARAM &cPar)
-{
+void BSLMM::CopyFromParam (PARAM &cPar) {
a_mode=cPar.a_mode;
d_pace=cPar.d_pace;
@@ -101,9 +100,7 @@ void BSLMM::CopyFromParam (PARAM &cPar)
return;
}
-
-void BSLMM::CopyToParam (PARAM &cPar)
-{
+void BSLMM::CopyToParam (PARAM &cPar) {
cPar.time_UtZ=time_UtZ;
cPar.time_Omega=time_Omega;
cPar.time_Proposal=time_Proposal;
@@ -115,16 +112,16 @@ void BSLMM::CopyToParam (PARAM &cPar)
return;
}
-
-
-void BSLMM::WriteBV (const gsl_vector *bv)
-{
+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;}
+ 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) {
@@ -132,7 +129,8 @@ void BSLMM::WriteBV (const gsl_vector *bv)
outfile<<"NA"<<endl;
}
else {
- outfile<<scientific<<setprecision(6)<<gsl_vector_get(bv, t)<<endl;
+ outfile<<scientific<<setprecision(6)<<
+ gsl_vector_get(bv, t)<<endl;
t++;
}
}
@@ -142,17 +140,16 @@ void BSLMM::WriteBV (const gsl_vector *bv)
return;
}
-
-
-
-void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector *alpha, const size_t w)
-{
+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;}
+ if (!outfile) {
+ cout<<"error writing file: "<<file_str.c_str()<<endl;
+ return;}
outfile<<"chr"<<"\t"<<"rs"<<"\t"
<<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t"
@@ -163,11 +160,13 @@ void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector
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";
+ <<snpInfo[i].base_position<<"\t"<<snpInfo[i].n_miss<<"\t";
- outfile<<scientific<<setprecision(6)<<gsl_vector_get(alpha, t)<<"\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;
+ 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;
@@ -180,15 +179,16 @@ void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector
return;
}
-
-void BSLMM::WriteParam (const gsl_vector *alpha)
-{
+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;}
+ if (!outfile) {
+ cout<<"error writing file: "<<file_str.c_str()<<endl;
+ return;
+ }
outfile<<"chr"<<"\t"<<"rs"<<"\t"
<<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t"
@@ -198,9 +198,10 @@ void BSLMM::WriteParam (const gsl_vector *alpha)
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<<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++;
}
@@ -210,9 +211,8 @@ void BSLMM::WriteParam (const gsl_vector *alpha)
return;
}
-
-void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl_matrix *Result_gamma, const size_t w_col)
-{
+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";
@@ -224,8 +224,14 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl
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;}
+ 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;
@@ -237,8 +243,14 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl
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;}
+ 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;}
@@ -247,16 +259,19 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl
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)<<
+ 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<<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<<
+ (int)gsl_matrix_get(Result_gamma,i,j)<<"\t";
}
outfile_gamma<<endl;
}
@@ -270,13 +285,11 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl
return;
}
-
-
-void BSLMM::CalcPgamma (double *p_gamma)
-{
+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=0.7*gsl_ran_geometric_pdf (i+1, 1.0/geo_mean)+0.3/
+ (double)ns_test;
p_gamma[i]=p;
s+=p;
}
@@ -287,10 +300,8 @@ void BSLMM::CalcPgamma (double *p_gamma)
return;
}
-
-
-void BSLMM::SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X, vector<size_t> &rank)
-{
+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]];
@@ -302,10 +313,8 @@ void BSLMM::SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X, vector<size_t> &
return;
}
-
-
-double BSLMM::CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const double sigma_a2)
-{
+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);
@@ -333,9 +342,9 @@ double BSLMM::CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty, cons
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)
-{
+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;
@@ -362,7 +371,8 @@ void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, vector<si
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);
+ 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);
}
@@ -379,18 +389,6 @@ void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, vector<si
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;
@@ -399,10 +397,9 @@ void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, vector<si
return;
}
-
-
-double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gsl_vector *Utu, gsl_vector *alpha_prime, class HYPBSLMM &cHyp)
-{
+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);
@@ -420,25 +417,28 @@ double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gs
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));
+ gsl_vector_set (Utu_rand, i,
+ gsl_ran_gaussian(gsl_r, 1)*sqrt(ds));
}
- //sample tau
+ // 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); }
+ if (a_mode==11) {
+ tau = gsl_ran_gamma (gsl_r, (double)ni_test/2.0, 2.0/Hi_yy);
+ }
- //sample alpha
+ // Sample alpha.
gsl_vector_memcpy (alpha_prime, Uty);
gsl_vector_mul (alpha_prime, weight_Hi);
gsl_vector_scale (alpha_prime, sigma_b2);
- //sample u
+ // 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
+ // For quantitative traits, calculate pve and ppe.
if (a_mode==11) {
gsl_blas_ddot (Utu, Utu, &d);
cHyp.pve=d/(double)ni_test;
@@ -446,12 +446,13 @@ double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gs
cHyp.pge=0.0;
}
- //calculate likelihood
+ // 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));
+ 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);
@@ -459,18 +460,22 @@ double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gs
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)
-{
+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_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 *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);
@@ -481,7 +486,8 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
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);
+ 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);
@@ -492,10 +498,10 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
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));
+ gsl_vector_set(Utu_rand,i,gsl_ran_gaussian(gsl_r,1)*sqrt(ds));
}
- //calculate Omega
+ // Calculate Omega.
gsl_matrix_set_identity (Omega);
time_start=clock();
@@ -504,8 +510,8 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
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);
+ // Calculate beta_hat.
+ gsl_blas_dgemv (CblasTrans, 1.0, UtXgamma_eval, Uty, 0.0, XtHiy);
logdet_O=CholeskySolve(Omega, XtHiy, beta_hat);
@@ -514,11 +520,13 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
gsl_blas_ddot (XtHiy, beta_hat, &d);
P_yy-=d;
- //sample tau
+ // 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); }
+ if (a_mode==11) {
+ tau =gsl_ran_gamma (gsl_r, (double)ni_test/2.0, 2.0/P_yy);
+ }
- //sample beta
+ // Sample beta.
for (size_t i=0; i<beta->size; i++)
{
d=gsl_ran_gaussian(gsl_r, 1);
@@ -526,27 +534,25 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
}
gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega, beta);
-
- //it compuates inv(L^T(Omega)) %*% beta;
+ // This computes 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
+ // 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
+ // 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
+ // For quantitative traits, calculate pve and pge.
if (a_mode==11) {
gsl_blas_ddot (UtXb, UtXb, &d);
cHyp.pge=d/(double)ni_test;
@@ -558,7 +564,6 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
else {cHyp.pge/=cHyp.pve;}
cHyp.pve/=cHyp.pve+1.0/tau;
}
-
gsl_matrix_free (UtXgamma_eval);
gsl_matrix_free (Omega);
@@ -570,17 +575,15 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
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));
+ 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)
-{
+// 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);
@@ -594,10 +597,10 @@ void BSLMM::CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *Utu, gsl_vector
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)
-{
+// 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);
@@ -620,18 +623,17 @@ void BSLMM::CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *UtXb, const gsl
return;
}
-
-
-
-void BSLMM::SampleZ (const gsl_vector *y, const gsl_vector *z_hat, gsl_vector *z)
-{
+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
+
+ // y is centered for case control studies.
if (d1<=0.0) {
- //control, right truncated
+
+ // Control, right truncated.
do {
z_rand=d2+gsl_ran_gaussian(gsl_r, 1.0);
} while (z_rand>0.0);
@@ -648,12 +650,8 @@ void BSLMM::SampleZ (const gsl_vector *y, const gsl_vector *z_hat, gsl_vector *z
return;
}
-
-
-
-
-double BSLMM::ProposeHnRho (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat)
-{
+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;
@@ -668,30 +666,13 @@ double BSLMM::ProposeHnRho (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp
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 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;
@@ -700,36 +681,25 @@ double BSLMM::ProposePi (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_ne
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;}
-
+ 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)
-{
+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)
-{
+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;
@@ -752,11 +722,19 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
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 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;
+ if(flag_gamma==1) {
+
+ // Add a SNP.
do {
r_add=gsl_ran_discrete (gsl_r, gsl_t);
} while (mapRank2in.count(r_add)!=0);
@@ -770,10 +748,13 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
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);
+ 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);
+ 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;
@@ -785,13 +766,17 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
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);
+ 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);
+ 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
+
+ // Be careful with the proposal.
do {
r_add=gsl_ran_discrete (gsl_r, gsl_t);
} while (mapRank2in.count(r_add)!=0);
@@ -802,7 +787,8 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
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_remove]/
+ (prob_total+p_gamma[r_remove]-p_gamma[r_add]));
logp-=log(p_gamma[r_add]/prob_total);
mapRank2in.erase(r_remove);
@@ -810,7 +796,7 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
rank_new.erase(rank_new.begin()+col_id);
rank_new.push_back(r_add);
}
- else {logp+=0;}//do not change
+ else {logp+=0;} // Do not change.
}
stable_sort (rank_new.begin(), rank_new.end(), comp_vec);
@@ -819,24 +805,14 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
return logp;
}
-
-
-
-
-
-bool comp_lr (pair<size_t, double> a, pair<size_t, double> b)
-{
+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) {
+// 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;
@@ -890,9 +866,10 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
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;
+ // 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)
{
@@ -900,7 +877,8 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
time (&rawtime);
tm * ptm = gmtime (&rawtime);
- randseed = (unsigned) (ptm->tm_hour%24*3600+ptm->tm_min*60+ptm->tm_sec);
+ 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);
@@ -910,17 +888,14 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
gsl_t=gsl_ran_discrete_preproc (ns_test, p_gamma);
- //initial parameters
+ // 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);
+ 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) {
@@ -928,10 +903,12 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
}
}
else {
- gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp_old.n_gamma);
+ 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);
+ 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) {
@@ -941,7 +918,7 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
gsl_vector_free (beta);
}
- //calculate centered z_hat, and pve
+ // Calculate centered z_hat, and pve.
if (a_mode==13) {
time_start=clock();
if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) {
@@ -953,15 +930,17 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
time_UtZ+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
}
- //start MCMC
+ // 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 (t%d_pace==0 || t==total_step-1) {
+ ProgressBar ("Running MCMC ", t, total_step-1,
+ (double)n_accept/(double)(t*n_mh+1));
+ }
if (a_mode==13) {
SampleZ (y, z_hat, z);
@@ -969,60 +948,75 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
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);
+ 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);
+ // 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);
+ 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);
+ 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));
+ beta_old.push_back(gsl_vector_get(beta, i));
}
gsl_matrix_free (UtXgamma);
gsl_vector_free (beta);
}
}
- //MH steps
+ // M-H 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;}
+ 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+=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);
+ 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);
+ 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);
+ 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));
+ beta_new.push_back(gsl_vector_get(beta, i));
}
gsl_matrix_free (UtXgamma);
gsl_vector_free (beta);
@@ -1030,17 +1024,20 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
logMHratio+=logPost_new-logPost_old;
- if (logMHratio>0 || log(gsl_rng_uniform(gsl_r))<logMHratio) {accept=1; n_accept++;}
+ 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]);
- }
+ 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);
@@ -1050,51 +1047,58 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
else {cHyp_new=cHyp_old;}
}
- //calculate z_hat, and pve
+ // 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);
+ CalcCC_PVEnZ (U, UtXb_old, Utu_old,
+ z_hat, cHyp_old);
}
- //sample mu and update z hat
+ // 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) );
-
+ 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);
+ time_UtZ+=(clock()-time_start)/
+ (double(CLOCKS_PER_SEC)*60.0);
}
- //Save data
+ // 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);}
+ 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);
+ 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);
+ 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);
+ gsl_matrix_set(Result_gamma,w_col,i,
+ pos);
beta_g[pos-1].first+=beta_old[i];
beta_g[pos-1].second+=1.0;
@@ -1138,7 +1142,8 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
}
gsl_vector *alpha=gsl_vector_alloc (ns_test);
- gsl_blas_dgemv (CblasTrans, 1.0/(double)ns_test, UtX, alpha_prime, 0.0, alpha);
+ gsl_blas_dgemv (CblasTrans, 1.0/(double)ns_test, UtX,
+ alpha_prime, 0.0, alpha);
WriteParam (beta_g, alpha, w);
gsl_vector_free(alpha);
@@ -1154,10 +1159,9 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
return;
}
-
-
-void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *eval, const double lambda)
-{
+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);
@@ -1169,7 +1173,8 @@ void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector
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_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);
@@ -1183,28 +1188,13 @@ void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector
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)
-{
+// 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_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);
@@ -1217,29 +1207,34 @@ void BSLMM::CalcXtX (const gsl_matrix *X, const gsl_vector *y, const size_t s_si
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)
-{
+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
+ // rank_old and rank_new are sorted already inside PorposeGamma
+ // calculate vectors rank_remove and rank_add.
+ // 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> 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());
+ 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());
+ 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());
+ 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 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;
@@ -1248,16 +1243,23 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
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
+ // 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);
@@ -1295,13 +1297,13 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
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
+ // Get X_add.
SetXgamma (X_add, X, rank_add);
- //get t(X_add)X_add and t(X_add)X_temp
+ // 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
+ // Somehow the lapack_dgemm does not work here.
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,
@@ -1310,18 +1312,26 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
- //save to X_new, XtX_new and Xty_new
+ // 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;}
+ 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_const_view Xcopy_col=
+ gsl_matrix_const_column(X_old, i_old);
gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector);
}
@@ -1334,8 +1344,15 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
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 (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);
@@ -1372,37 +1389,40 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
return;
}
-
-double BSLMM::CalcPosterior (const double yty, class HYPBSLMM &cHyp)
-{
+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
+ // 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
+ // 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));
+ 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 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_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);
@@ -1411,38 +1431,42 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX, co
gsl_vector_memcpy (Xty_temp, &Xty_sub.vector);
- //calculate Omega
+ // 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
+ // 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
+ // 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); }
+ if (a_mode==11) {
+ tau = gsl_ran_gamma (gsl_r, (double)ni_test/2.0, 2.0/P_yy);
+ }
- //sample beta
+ // 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);
+ gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega,
+ &beta_sub.vector);
- //it compuates inv(L^T(Omega)) %*% beta;
+ // This computes 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);
+ gsl_blas_dgemv (CblasNoTrans, 1.0, &Xgamma_sub.matrix,
+ &beta_sub.vector, 0.0, Xb);
- //for quantitative traits, calculate pve and pge
+ // For quantitative traits, calculate pve and pge.
if (a_mode==11) {
gsl_blas_ddot (Xb, Xb, &d);
cHyp.pve=d/(double)ni_test;
@@ -1454,7 +1478,8 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX, co
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));
+ 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);
@@ -1464,9 +1489,7 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX, co
return logpost;
}
-
-
-//calculate pve and pge, and calculate z_hat for case-control data
+// 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);
@@ -1475,10 +1498,9 @@ void BSLMM::CalcCC_PVEnZ (gsl_vector *z_hat, class HYPBSLMM &cHyp)
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)
-{
+// 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);
@@ -1491,9 +1513,7 @@ void BSLMM::CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat, class HYPBSLM
return;
}
-
-
-//if a_mode==13, then run probit model
+// 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;
@@ -1520,7 +1540,9 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
double ztz=0.0;
gsl_vector_memcpy (z, y);
- //for quantitative traits, y is centered already in gemma.cpp, but just in case
+
+ // 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);
@@ -1549,9 +1571,10 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
mapRank2pos[i]=pos_loglr[i].first;
}
- //calculate proposal distribution for gamma (unnormalized), and set up gsl_r and gsl_t
+ // Calculate proposal distribution for gamma (unnormalized),
+ // and set up gsl_r and gsl_t.
gsl_rng_env_setup();
- const gsl_rng_type * gslType;
+ const gsl_rng_type * gslType;
gslType = gsl_rng_default;
if (randseed<0)
{
@@ -1559,7 +1582,8 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
time (&rawtime);
tm * ptm = gmtime (&rawtime);
- randseed = (unsigned) (ptm->tm_hour%24*3600+ptm->tm_min*60+ptm->tm_sec);
+ 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);
@@ -1569,7 +1593,7 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
gsl_t=gsl_ran_discrete_preproc (ns_test, p_gamma);
- //initial parameters
+ // Initial parameters.
InitialMCMC (X, z, rank_old, cHyp_old, pos_loglr);
cHyp_initial=cHyp_old;
@@ -1580,10 +1604,12 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
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);
+ 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
+ // Calculate centered z_hat, and pve.
if (a_mode==13) {
if (cHyp_old.n_gamma==0) {
CalcCC_PVEnZ (z_hat, cHyp_old);
@@ -1593,65 +1619,94 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
}
}
- //start MCMC
+ // 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 (t%d_pace==0 || t==total_step-1) {
+ ProgressBar ("Running MCMC ", t, total_step-1,
+ (double)n_accept/(double)(t*n_mh+1));
+ }
+
if (a_mode==13) {
SampleZ (y, z_hat, z);
mean_z=CenterVector (z);
gsl_blas_ddot(z,z,&ztz);
- //First proposal
+ // 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);
+ 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
+ // M-H 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);}
+ 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+=
+ 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
+
+ // This 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);
+ 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);
+ 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);
+ 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++;}
+ 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;
@@ -1659,8 +1714,10 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
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]);
+ 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());
@@ -1684,7 +1741,7 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
}
- //calculate z_hat, and pve
+ // Calculate z_hat, and pve.
if (a_mode==13) {
if (cHyp_old.n_gamma==0) {
CalcCC_PVEnZ (z_hat, cHyp_old);
@@ -1693,41 +1750,47 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
CalcCC_PVEnZ (Xb_old, z_hat, cHyp_old);
}
- //sample mu and update z hat
+ // 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) );
+ mean_z+=gsl_ran_gaussian(gsl_r,
+ sqrt(1.0/(double) ni_test));
gsl_vector_add_constant (z_hat, mean_z);
}
- //Save data
+ // 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);}
+ 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);
+ 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);
+ 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);
+ gsl_matrix_set(Result_gamma,w_col,
+ i,pos);
- beta_g[pos-1].first+=gsl_vector_get(beta_old, i);
+ beta_g[pos-1].first+=
+ gsl_vector_get(beta_old, i);
beta_g[pos-1].second+=1.0;
}
@@ -1736,9 +1799,7 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
}
w++;
-
}
-
}
}
cout<<endl;
diff --git a/src/bslmm.h b/src/bslmm.h
index 07aac67..da185fa 100644
--- a/src/bslmm.h
+++ b/src/bslmm.h
@@ -40,96 +40,140 @@ public:
string file_out;
string path_out;
- // LMM related parameters
+ // 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
- double logp_min, logp_max, logp_scale; //priors for log(pi)
- size_t s_min, s_max; //minimum and maximum number of gammas
- size_t w_step; //number of warm up/burn in iterations
- size_t s_step; //number of sampling iterations
- size_t r_pace; //record pace
- size_t w_pace; //write pace
- size_t n_accept; //number of acceptance
- size_t n_mh; //number of MH steps within each iteration
- double geo_mean; //mean of the geometric distribution
+ // BSLMM MCMC-related parameters
+ double h_min, h_max, h_scale; // Priors for h.
+ double rho_min, rho_max, rho_scale; // Priors for rho.
+ double logp_min, logp_max, logp_scale; // Priors for log(pi).
+ size_t s_min, s_max; // Min. & max. number of gammas.
+ size_t w_step; // Number of warm up/burn in
+ // iterations.
+ size_t s_step; // Num. sampling iterations.
+ size_t r_pace; // Record pace.
+ size_t w_pace; // Write pace.
+ size_t n_accept; // Number of acceptances.
+ size_t n_mh; // Number of MH steps per iter.
+ double geo_mean; // Mean of geometric dist.
long int randseed;
double trace_G;
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 n_cvt; //number of covariates
+ // Summary statistics.
+ size_t ni_total, ns_total; // Number of total individuals and SNPs
+ size_t ni_test, ns_test; // Num. individuals & SNPs used in analysis.
+ size_t n_cvt; // Number of covariates.
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
-
- vector<SNPINFO> snpInfo; //record SNP information
+ double time_Omega; // Time spent on optimization iterations.
+
+ // Time spent on constructing the proposal distribution for
+ // gamma (i.e. lmm or lm analysis).
+ double time_Proposal;
+
+ // 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;
+
+ // Record SNP information.
+ vector<SNPINFO> snpInfo;
- // Not included in PARAM
+ // Not included in PARAM.
gsl_rng *gsl_r;
gsl_ran_discrete_t *gsl_t;
map<size_t, size_t> mapRank2pos;
- // Main Functions
+ // 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 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);
+ void MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
+ const gsl_vector *Uty, const gsl_vector *K_eval,
+ const gsl_vector *y);
void WriteLog ();
void WriteLR ();
void WriteBV (const gsl_vector *bv);
- void WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector *alpha, const size_t w);
+ void WriteParam (vector<pair<double, double> > &beta_g,
+ const gsl_vector *alpha, const size_t w);
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);
+ void WriteResult (const int flag, const gsl_matrix *Result_hyp,
+ const gsl_matrix *Result_gamma, const size_t w_col);
- //Subfunctions inside MCMC
+ // 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, vector<size_t> &rank_old, class HYPBSLMM &cHyp, vector<pair<size_t, double> > &pos_loglr);
- double CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gsl_vector *Utu, gsl_vector *alpha_prime, class HYPBSLMM &cHyp);
- double 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);
- void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *Utu, gsl_vector *z_hat, class HYPBSLMM &cHyp);
- void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *UtXb, const gsl_vector *Utu, gsl_vector *z_hat, class HYPBSLMM &cHyp);
- double CalcREMLE (const gsl_matrix *Utw, const gsl_vector *Uty, const gsl_vector *K_eval);
- double CalcLR (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, vector<pair<size_t, double> > &loglr_sort); //calculate the maximum marginal likelihood ratio for each analyzed SNPs with gemma, use it to rank SNPs
- void SampleZ (const gsl_vector *y, const gsl_vector *z_hat, gsl_vector *z);
- double ProposeHnRho (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat);
- double ProposePi (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat);
- double 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);
- void SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X, vector<size_t> &rank);
-
- void CalcXtX (const gsl_matrix *X_new, const gsl_vector *y, const size_t s_size, gsl_matrix *XtX_new, gsl_vector *Xty_new);
- void 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 CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
+ const double sigma_a2);
+ void InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty,
+ vector<size_t> &rank_old, class HYPBSLMM &cHyp,
+ vector<pair<size_t, double> > &pos_loglr);
+ double CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval,
+ gsl_vector *Utu, gsl_vector *alpha_prime,
+ class HYPBSLMM &cHyp);
+ double 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);
+ void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *Utu,
+ gsl_vector *z_hat, class HYPBSLMM &cHyp);
+ void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *UtXb,
+ const gsl_vector *Utu, gsl_vector *z_hat,
+ class HYPBSLMM &cHyp);
+ double CalcREMLE (const gsl_matrix *Utw, const gsl_vector *Uty,
+ const gsl_vector *K_eval);
+
+ // Calculate the maximum marginal likelihood ratio for each
+ // analyzed SNPs with gemma, use it to rank SNPs.
+ double CalcLR (const gsl_matrix *U, const gsl_matrix *UtX,
+ const gsl_vector *Uty, const gsl_vector *K_eval,
+ vector<pair<size_t, double> > &loglr_sort);
+ void SampleZ (const gsl_vector *y, const gsl_vector *z_hat,
+ gsl_vector *z);
+ double ProposeHnRho (const class HYPBSLMM &cHyp_old,
+ class HYPBSLMM &cHyp_new, const size_t &repeat);
+ double ProposePi (const class HYPBSLMM &cHyp_old,
+ class HYPBSLMM &cHyp_new,
+ const size_t &repeat);
+ double 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);
+ void SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X,
+ vector<size_t> &rank);
+
+ void CalcXtX (const gsl_matrix *X_new, const gsl_vector *y,
+ const size_t s_size, gsl_matrix *XtX_new,
+ gsl_vector *Xty_new);
+ void 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 CalcPosterior (const double yty, class HYPBSLMM &cHyp);
- double 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 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);
void CalcCC_PVEnZ (gsl_vector *z_hat, class HYPBSLMM &cHyp);
- void CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat, class HYPBSLMM &cHyp);
+ void CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat,
+ class HYPBSLMM &cHyp);
void MCMC (const gsl_matrix *X, const gsl_vector *y);
-
- //utility functions
-// double vec_sum (gsl_vector *v);
-// void vec_center (gsl_vector *v);
-// double calc_var (gsl_vector *v);
-// void calc_sigma (MCMC &cMcmc);
-// bool comp_lr (pair<size_t, double> a, pair<size_t, double> b);
};
-
-
#endif
diff --git a/src/bslmmdap.cpp b/src/bslmmdap.cpp
index e1b20d8..ebbff70 100644
--- a/src/bslmmdap.cpp
+++ b/src/bslmmdap.cpp
@@ -49,8 +49,7 @@
using namespace std;
-void BSLMMDAP::CopyFromParam (PARAM &cPar)
-{
+void BSLMMDAP::CopyFromParam (PARAM &cPar) {
file_out=cPar.file_out;
path_out=cPar.path_out;
@@ -83,9 +82,7 @@ void BSLMMDAP::CopyFromParam (PARAM &cPar)
return;
}
-
-void BSLMMDAP::CopyToParam (PARAM &cPar)
-{
+void BSLMMDAP::CopyToParam (PARAM &cPar) {
cPar.time_UtZ=time_UtZ;
cPar.time_Omega=time_Omega;
@@ -94,13 +91,16 @@ void BSLMMDAP::CopyToParam (PARAM &cPar)
-//read hyp file
-void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2, vector<double> &vec_sb2, vector<double> &vec_wab)
-{
+// Read hyp file.
+void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2,
+ vector<double> &vec_sb2, vector<double> &vec_wab) {
vec_sa2.clear(); vec_sb2.clear(); vec_wab.clear();
igzstream infile (file_hyp.c_str(), igzstream::in);
- if (!infile) {cout<<"error! fail to open hyp file: "<<file_hyp<<endl; return;}
+ if (!infile) {
+ cout<<"error! fail to open hyp file: "<<file_hyp<<endl;
+ return;
+ }
string line;
char *ch_ptr;
@@ -127,10 +127,9 @@ void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2, vector<doubl
return;
}
-
-//read bf file
-void ReadFile_bf (const string &file_bf, vector<string> &vec_rs, vector<vector<vector<double> > > &BF)
-{
+// Read bf file.
+void ReadFile_bf (const string &file_bf, vector<string> &vec_rs,
+ vector<vector<vector<double> > > &BF) {
BF.clear(); vec_rs.clear();
igzstream infile (file_bf.c_str(), igzstream::in);
@@ -172,7 +171,9 @@ void ReadFile_bf (const string &file_bf, vector<string> &vec_rs, vector<vector<v
if (t==0) {
bf_size=vec_bf.size();
} else {
- if (bf_size!=vec_bf.size()) {cout<<"error! unequal row size in bf file."<<endl;}
+ if (bf_size!=vec_bf.size()) {
+ cout<<"error! unequal row size in bf file."<<endl;
+ }
}
if (flag_block==0) {
@@ -193,24 +194,28 @@ void ReadFile_bf (const string &file_bf, vector<string> &vec_rs, vector<vector<v
}
-//read category files
-//read both continuous and discrete category file, record mapRS2catc
-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)
-{
+// Read category files.
+// Read both continuous and discrete category file, record mapRS2catc.
+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) {
igzstream infile (file_cat.c_str(), igzstream::in);
- if (!infile) {cout<<"error! fail to open category file: "<<file_cat<<endl; return;}
+ if (!infile) {
+ cout<<"error! fail to open category file: "<<file_cat<<endl;
+ return;
+ }
string line;
char *ch_ptr;
string rs, chr, a1, a0, pos, cm;
- //read header
+ // Read header.
HEADER header;
!safeGetline(infile, line).eof();
ReadHeader_io (line, header);
- //use the header to determine the number of categories
+ // Use the header to determine the number of categories.
kc=header.catc_col.size(); kd=header.catd_col.size();
//set up storage and mapper
@@ -219,7 +224,7 @@ void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs, gsl_mat
vector<double> catc;
vector<int> catd;
- //read the following lines to record mapRS2cat
+ // Read the following lines to record mapRS2cat.
while (!safeGetline(infile, line).eof()) {
ch_ptr=strtok ((char *)line.c_str(), " , \t");
@@ -255,7 +260,7 @@ void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs, gsl_mat
if (mapRS2catd.count(rs)==0 && kd>0) {mapRS2catd[rs]=catd;}
}
- //load into Ad and Ac
+ // Load into Ad and Ac.
if (kc>0) {
Ac=gsl_matrix_alloc(vec_rs.size(), kc);
for (size_t i=0; i<vec_rs.size(); i++) {
@@ -305,15 +310,7 @@ void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs, gsl_mat
return;
}
-
-
-
-
-
-
-
-void BSLMMDAP::WriteResult (const gsl_matrix *Hyper, const gsl_matrix *BF)
-{
+void BSLMMDAP::WriteResult (const gsl_matrix *Hyper, const gsl_matrix *BF) {
string file_bf, file_hyp;
file_bf=path_out+"/"+file_out;
file_bf+=".bf.txt";
@@ -325,10 +322,17 @@ void BSLMMDAP::WriteResult (const gsl_matrix *Hyper, const gsl_matrix *BF)
outfile_bf.open (file_bf.c_str(), ofstream::out);
outfile_hyp.open (file_hyp.c_str(), ofstream::out);
- if (!outfile_bf) {cout<<"error writing file: "<<file_bf<<endl; return;}
- if (!outfile_hyp) {cout<<"error writing file: "<<file_hyp<<endl; return;}
+ if (!outfile_bf) {
+ cout<<"error writing file: "<<file_bf<<endl;
+ return;
+ }
+ if (!outfile_hyp) {
+ cout<<"error writing file: "<<file_hyp<<endl;
+ return;
+ }
- outfile_hyp<<"h"<<"\t"<<"rho"<<"\t"<<"sa2"<<"\t"<<"sb2"<<"\t"<<"weight"<<endl;
+ outfile_hyp<<"h"<<"\t"<<"rho"<<"\t"<<"sa2"<<"\t"<<"sb2"<<"\t"<<
+ "weight"<<endl;
outfile_hyp<<scientific;
for (size_t i=0; i<Hyper->size1; i++) {
for (size_t j=0; j<Hyper->size2; j++) {
@@ -366,10 +370,9 @@ void BSLMMDAP::WriteResult (const gsl_matrix *Hyper, const gsl_matrix *BF)
return;
}
-
-
-void BSLMMDAP::WriteResult (const vector<string> &vec_rs, const gsl_matrix *Hyper, const gsl_vector *pip, const gsl_vector *coef)
-{
+void BSLMMDAP::WriteResult (const vector<string> &vec_rs,
+ const gsl_matrix *Hyper, const gsl_vector *pip,
+ const gsl_vector *coef) {
string file_gamma, file_hyp, file_coef;
file_gamma=path_out+"/"+file_out;
file_gamma+=".gamma.txt";
@@ -384,11 +387,21 @@ void BSLMMDAP::WriteResult (const vector<string> &vec_rs, const gsl_matrix *Hype
outfile_hyp.open (file_hyp.c_str(), ofstream::out);
outfile_coef.open (file_coef.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;}
- if (!outfile_coef) {cout<<"error writing file: "<<file_coef<<endl; return;}
+ if (!outfile_gamma) {
+ cout<<"error writing file: "<<file_gamma<<endl;
+ return;
+ }
+ if (!outfile_hyp) {
+ cout<<"error writing file: "<<file_hyp<<endl;
+ return;
+ }
+ if (!outfile_coef) {
+ cout<<"error writing file: "<<file_coef<<endl;
+ return;
+ }
- outfile_hyp<<"h"<<"\t"<<"rho"<<"\t"<<"sa2"<<"\t"<<"sb2"<<"\t"<<"weight"<<endl;
+ outfile_hyp<<"h"<<"\t"<<"rho"<<"\t"<<"sa2"<<"\t"<<"sb2"<<"\t"<<
+ "weight"<<endl;
outfile_hyp<<scientific;
for (size_t i=0; i<Hyper->size1; i++) {
for (size_t j=0; j<Hyper->size2; j++) {
@@ -397,10 +410,10 @@ void BSLMMDAP::WriteResult (const vector<string> &vec_rs, const gsl_matrix *Hype
outfile_hyp<<endl;
}
-
outfile_gamma<<"rs"<<"\t"<<"gamma"<<endl;
for (size_t i=0; i<vec_rs.size(); ++i) {
- outfile_gamma<<vec_rs[i]<<"\t"<<scientific<<setprecision(6)<<gsl_vector_get(pip, i)<<endl;
+ outfile_gamma<<vec_rs[i]<<"\t"<<scientific<<setprecision(6)<<
+ gsl_vector_get(pip, i)<<endl;
}
outfile_coef<<"coef"<<endl;
@@ -419,25 +432,9 @@ void BSLMMDAP::WriteResult (const vector<string> &vec_rs, const gsl_matrix *Hype
}
-
-
-/*
-void BSLMMDAP::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 BSLMMDAP::CalcMarginal (const gsl_vector *Uty, const gsl_vector *K_eval, const double sigma_b2, const double tau)
-{
+double BSLMMDAP::CalcMarginal (const gsl_vector *Uty,
+ const gsl_vector *K_eval,
+ const double sigma_b2, const double tau) {
gsl_vector *weight_Hi=gsl_vector_alloc (Uty->size);
double logm=0.0;
@@ -452,7 +449,7 @@ double BSLMMDAP::CalcMarginal (const gsl_vector *Uty, const gsl_vector *K_eval,
Hi_yy+=d*uy*uy;
}
- //calculate likelihood
+ // Calculate likelihood.
logm=-0.5*logdet_H-0.5*tau*Hi_yy+0.5*log(tau)*(double)ni_test;
gsl_vector_free (weight_Hi);
@@ -460,14 +457,17 @@ double BSLMMDAP::CalcMarginal (const gsl_vector *Uty, const gsl_vector *K_eval,
return logm;
}
-
-double BSLMMDAP::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 BSLMMDAP::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) {
clock_t time_start;
double logm=0.0;
double d, 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 *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);
@@ -477,7 +477,7 @@ double BSLMMDAP::CalcMarginal (const gsl_matrix *UtXgamma, const gsl_vector *Uty
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);
+ gsl_vector_view UtXgamma_row=gsl_matrix_row(UtXgamma_eval,i);
d=gsl_vector_get (K_eval, i)*sigma_b2;
d=1.0/(d+1.0);
gsl_vector_set (weight_Hi, i, d);
@@ -488,7 +488,7 @@ double BSLMMDAP::CalcMarginal (const gsl_matrix *UtXgamma, const gsl_vector *Uty
gsl_vector_scale (&UtXgamma_row.vector, d);
}
- //calculate Omega
+ // Calculate Omega.
gsl_matrix_set_identity (Omega);
time_start=clock();
@@ -496,7 +496,7 @@ double BSLMMDAP::CalcMarginal (const gsl_matrix *UtXgamma, const gsl_vector *Uty
UtXgamma, 1.0, Omega);
time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
- //calculate beta_hat
+ // Calculate beta_hat.
gsl_blas_dgemv (CblasTrans, 1.0, UtXgamma_eval, Uty, 0.0, XtHiy);
logdet_O=CholeskySolve(Omega, XtHiy, beta_hat);
@@ -512,24 +512,26 @@ double BSLMMDAP::CalcMarginal (const gsl_matrix *UtXgamma, const gsl_vector *Uty
gsl_vector_free (beta_hat);
gsl_vector_free (weight_Hi);
- logm=-0.5*logdet_H-0.5*logdet_O-0.5*tau*P_yy+0.5*log(tau)*(double)ni_test;
+ logm=-0.5*logdet_H-0.5*logdet_O-0.5*tau*P_yy+0.5*log(tau)*
+ (double)ni_test;
return logm;
}
-
double BSLMMDAP::CalcPrior (class HYPBSLMM &cHyp) {
double logprior=0;
- logprior=((double)cHyp.n_gamma-1.0)*cHyp.logp+((double)ns_test-(double)cHyp.n_gamma)*log(1.0-exp(cHyp.logp));
+ logprior=((double)cHyp.n_gamma-1.0)*cHyp.logp+
+ ((double)ns_test-(double)cHyp.n_gamma)*log(1.0-exp(cHyp.logp));
return logprior;
}
-
-//where A is the ni_test by n_cat matrix of annotations
-void BSLMMDAP::DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const gsl_vector *y) {
+// Where A is the ni_test by n_cat matrix of annotations.
+void BSLMMDAP::DAP_CalcBF (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;
- //set up BF
+ // Set up BF.
double tau, h, rho, sigma_a2, sigma_b2, d;
size_t ns_causal=10;
size_t n_grid=h_ngrid*rho_ngrid;
@@ -539,11 +541,13 @@ void BSLMMDAP::DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX, const gsl
gsl_matrix *Xgamma=gsl_matrix_alloc(ni_test, 1);
gsl_matrix *Hyper=gsl_matrix_alloc(n_grid, 5);
- //compute tau by using yty
+ // Compute tau by using yty.
gsl_blas_ddot (Uty, Uty, &tau);
tau=(double)ni_test/tau;
- //set up grid values for sigma_a2 and sigma_b2 based on an approximately even grid for h and rho, and a fixed number of causals
+ // Set up grid values for sigma_a2 and sigma_b2 based on an
+ // approximately even grid for h and rho, and a fixed number
+ // of causals.
size_t ij=0;
for (size_t i=0; i<h_ngrid; i++) {
h=h_min+(h_max-h_min)*(double)i/((double)h_ngrid-1);
@@ -566,7 +570,7 @@ void BSLMMDAP::DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX, const gsl
}
}
- //compute BF factors
+ // Compute BF factors.
time_start=clock();
cout<<"Calculating BF..."<<endl;
for (size_t t=0; t<ns_test; t++) {
@@ -587,21 +591,20 @@ void BSLMMDAP::DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX, const gsl
}
time_Proposal=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
- //save results
+ // Save results.
WriteResult (Hyper, BF);
- //free matrices and vectors
+ // Free matrices and vectors.
gsl_matrix_free(BF);
gsl_matrix_free(Xgamma);
gsl_matrix_free(Hyper);
return;
}
-
-
-
-
-void single_ct_regression(const gsl_matrix_int *Xd, const gsl_vector_int *dlevel, const gsl_vector *pip_vec, gsl_vector *coef, gsl_vector *prior_vec) {
+void single_ct_regression(const gsl_matrix_int *Xd,
+ const gsl_vector_int *dlevel,
+ const gsl_vector *pip_vec,
+ gsl_vector *coef, gsl_vector *prior_vec) {
map<int,double> sum_pip;
map<int,double> sum;
@@ -623,27 +626,26 @@ void single_ct_regression(const gsl_matrix_int *Xd, const gsl_vector_int *dlevel
gsl_vector_set(prior_vec,i,sum_pip[cat]/sum[cat]);
}
- //double baseline=0;
for(int i=0;i<levels;i++){
double new_prior = sum_pip[i]/sum[i];
- //gsl_vector_set(coef, i, log(new_prior/(1-new_prior))-baseline);
- //if(i==0){
- //baseline = log(new_prior/(1-new_prior));
- //}
gsl_vector_set(coef, i, log(new_prior/(1-new_prior)) );
}
return;
}
-
-
-
-//where A is the ni_test by n_cat matrix of annotations
-void BSLMMDAP::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) {
+// Where A is the ni_test by n_cat matrix of annotations.
+void BSLMMDAP::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) {
clock_t time_start;
- //set up BF
+ // Set up BF.
double h, rho, sigma_a2, sigma_b2, d, s, logm, logm_save;
size_t t1, t2;
size_t n_grid=wab.size(), ns_test=vec_rs.size();
@@ -653,10 +655,10 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
gsl_vector *pip=gsl_vector_alloc(ns_test);
gsl_vector *coef=gsl_vector_alloc(kc+kd+1);
- //perform the EM algorithm
+ // Perform the EM algorithm.
vector<double> vec_wab, vec_wab_new;
- //initial values
+ // Initial values.
for (size_t t=0; t<ns_test; t++) {
gsl_vector_set (prior_vec, t, (double)BF.size()/(double)ns_test);
}
@@ -665,11 +667,12 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
vec_wab_new.push_back(wab[ij]);
}
- //EM iteration
+ // EM iteration.
size_t it=0;
double dif=1;
while (it<100 && dif>1e-3) {
- //update E_gamma
+
+ // Update E_gamma.
t1=0, t2=0;
for (size_t b=0; b<BF.size(); b++) {
s=1;
@@ -678,7 +681,7 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
for (size_t ij=0; ij<n_grid; ij++) {
d+=vec_wab_new[ij]*BF[b][m][ij];
}
- d*=gsl_vector_get(prior_vec, t1)/(1-gsl_vector_get(prior_vec, t1));
+ d*=gsl_vector_get(prior_vec,t1)/(1-gsl_vector_get(prior_vec,t1));
gsl_vector_set(pip, t1, d);
s+=d;
@@ -692,7 +695,7 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
}
}
- //update E_wab
+ // Update E_wab.
s=0;
for (size_t ij=0; ij<n_grid; ij++) {
vec_wab_new[ij]=0;
@@ -701,7 +704,8 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
for (size_t b=0; b<BF.size(); b++) {
d=1;
for (size_t m=0; m<BF[b].size(); m++) {
- d+=gsl_vector_get(prior_vec, t1)/(1-gsl_vector_get(prior_vec, t1))*vec_wab[ij]*BF[b][m][ij];
+ d+=gsl_vector_get(prior_vec, t1)/
+ (1-gsl_vector_get(prior_vec, t1))*vec_wab[ij]*BF[b][m][ij];
t1++;
}
vec_wab_new[ij]+=log(d);
@@ -718,11 +722,12 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
for (size_t ij=0; ij<n_grid; ij++) {
vec_wab_new[ij]/=d;
- // vec_wab[ij]=vec_wab_new[ij];
}
- //update coef, and pi
- if(kc==0 && kd==0){//no annotation
+ // Update coef, and pi.
+ if(kc==0 && kd==0){
+
+ // No annotation.
s=0;
for (size_t t=0; t<pip->size; t++) {
s+=gsl_vector_get(pip, t);
@@ -733,22 +738,28 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
}
gsl_vector_set (coef, 0, log(s/(1-s)));
- } else if(kc==0 && kd!=0){//only discrete annotations
+ } else if(kc==0 && kd!=0){
+
+ // Only discrete annotations.
if(kd == 1){
single_ct_regression(Ad, dlevel, pip, coef, prior_vec);
}else{
logistic_cat_fit(coef, Ad, dlevel, pip, 0, 0);
logistic_cat_pred(coef, Ad, dlevel, prior_vec);
}
- } else if (kc!=0 && kd==0) {//only continuous annotations
+ } else if (kc!=0 && kd==0) {
+
+ // Only continuous annotations.
logistic_cont_fit(coef, Ac, pip, 0, 0);
logistic_cont_pred(coef, Ac, prior_vec);
- } else if (kc!=0 && kd!=0) {//both continuous and categorical annotations
+ } else if (kc!=0 && kd!=0) {
+
+ // Both continuous and categorical annotations.
logistic_mixed_fit(coef, Ad, dlevel, Ac, pip, 0, 0);
logistic_mixed_pred(coef, Ad, dlevel, Ac, prior_vec);
}
- //compute marginal likelihood
+ // Compute marginal likelihood.
logm=0;
t1=0;
@@ -757,7 +768,8 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
for (size_t m=0; m<BF[b].size(); m++) {
s+=log(1-gsl_vector_get(prior_vec, t1));
for (size_t ij=0; ij<n_grid; ij++) {
- d+=gsl_vector_get(prior_vec, t1)/(1-gsl_vector_get(prior_vec, t1))*vec_wab[ij]*BF[b][m][ij];
+ d+=gsl_vector_get(prior_vec, t1)/
+ (1-gsl_vector_get(prior_vec, t1))*vec_wab[ij]*BF[b][m][ij];
}
}
logm+=log(d)+s;
@@ -773,14 +785,17 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
cout<<"iteration = "<<it<<"; marginal likelihood = "<<logm<<endl;
}
- //update h and rho that correspond to w_ab
+ // Update h and rho that correspond to w_ab.
for (size_t ij=0; ij<n_grid; ij++) {
sigma_a2=vec_sa2[ij];
sigma_b2=vec_sb2[ij];
- d=exp(gsl_vector_get(coef, coef->size-1))/(1+exp(gsl_vector_get(coef, coef->size-1)));
- h=(d*(double)ns_test*sigma_a2+1*sigma_b2)/(1+d*(double)ns_test*sigma_a2+1*sigma_b2);
- rho=d*(double)ns_test*sigma_a2/(d*(double)ns_test*sigma_a2+1*sigma_b2);
+ d=exp(gsl_vector_get(coef, coef->size-1))/
+ (1+exp(gsl_vector_get(coef, coef->size-1)));
+ h=(d*(double)ns_test*sigma_a2+1*sigma_b2)/
+ (1+d*(double)ns_test*sigma_a2+1*sigma_b2);
+ rho=d*(double)ns_test*sigma_a2/
+ (d*(double)ns_test*sigma_a2+1*sigma_b2);
gsl_matrix_set (Hyper, ij, 0, h);
gsl_matrix_set (Hyper, ij, 1, rho);
@@ -789,13 +804,12 @@ void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, const vector
gsl_matrix_set (Hyper, ij, 4, vec_wab_new[ij]);
}
- //obtain beta and alpha parameters
-
+ // Obtain beta and alpha parameters.
- //save results
+ // Save results.
WriteResult (vec_rs, Hyper, pip, coef);
- //free matrices and vectors
+ // Free matrices and vectors.
gsl_vector_free(prior_vec);
gsl_matrix_free(Hyper);
gsl_vector_free(pip);
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
diff --git a/src/gemma.h b/src/gemma.h
index acb1309..8393470 100644
--- a/src/gemma.h
+++ b/src/gemma.h
@@ -1,6 +1,6 @@
/*
- Genome-wide Efficient Mixed Model Association (GEMMA)
- Copyright (C) 2011 Xiang Zhou
+ 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
@@ -13,32 +13,28 @@
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/>.
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __GEMMA_H__
#define __GEMMA_H__
-#ifdef FORCE_FLOAT
-#include "param_float.h"
-#else
#include "param.h"
-#endif
using namespace std;
class GEMMA {
public:
- //parameters
+ // Parameters.
string version;
string date;
string year;
- //constructor
+ // Constructor.
GEMMA(void);
- //functions
+ // Functions.
void PrintHeader (void);
void PrintHelp (size_t option);
void PrintLicense (void);
@@ -47,6 +43,5 @@ public:
void WriteLog (int argc, char **argv, PARAM &cPar);
};
-
#endif
diff --git a/src/lmm.h b/src/lmm.h
index efbda4d..1e88cec 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -1,6 +1,6 @@
-/*
- Genome-wide Efficient Mixed Model Association (GEMMA)
- Copyright (C) 2011 Xiang Zhou
+/*
+ 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
@@ -13,7 +13,7 @@
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/>.
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __LMM_H__
@@ -21,22 +21,12 @@
#include "gsl/gsl_vector.h"
#include "gsl/gsl_matrix.h"
-
-
-#ifdef FORCE_FLOAT
-#include "param_float.h"
-#include "io_float.h"
-#else
#include "param.h"
#include "io.h"
-#endif
using namespace std;
-
-
-class FUNC_PARAM
-{
+class FUNC_PARAM {
public:
bool calc_null;
@@ -48,15 +38,12 @@ public:
size_t e_mode;
};
-
-
-
class LMM {
public:
- // IO related parameters
- int a_mode; //analysis mode, 1/2/3/4 for Frequentist tests
- size_t d_pace; //display pace
+ // 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;
@@ -75,42 +62,76 @@ public:
double logl_mle_H0;
// Summary statistics
- size_t ni_total, ni_test; //number of individuals
- size_t ns_total, ns_test; //number of snps
- size_t ng_total, ng_test; //number of genes
+ size_t ni_total, ni_test; // Number of individuals.
+ size_t ns_total, ns_test; // Number of SNPs.
+ size_t ng_total, ng_test; // Number of genes.
size_t n_cvt;
- double time_UtX; //time spent on optimization iterations
- double time_opt; //time spent on optimization iterations
+ double time_UtX; // Time spent on optimization iterations.
+ double time_opt; // Time spent on optimization iterations.
- 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
+ // Indicator for individuals (phenotypes): 0 missing, 1
+ // available for analysis.
+ vector<int> indicator_idv;
- vector<SNPINFO> snpInfo; //record SNP information
+ // Sequence indicator for SNPs: 0 ignored because of (a) maf,
+ // (b) miss, (c) non-poly; 1 available for analysis.
+ vector<int> indicator_snp;
- // Not included in PARAM
- vector<SUMSTAT> sumStat; //Output SNPSummary Data
+ vector<SNPINFO> snpInfo; // Record SNP information.
- // Main functions
+ // Not included in PARAM.
+ vector<SUMSTAT> sumStat; // Output SNPSummary Data.
+
+ // Main functions.
void CopyFromParam (PARAM &cPar);
void CopyToParam (PARAM &cPar);
- void AnalyzeGene (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Utx, const gsl_matrix *W, const gsl_vector *x);
- void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
- // WJA added
- void Analyzebgen (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
- void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
- void AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y, const gsl_vector *env);
- void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y, const gsl_vector *env);
+ void AnalyzeGene (const gsl_matrix *U, const gsl_vector *eval,
+ const gsl_matrix *UtW, const gsl_vector *Utx,
+ const gsl_matrix *W, const gsl_vector *x);
+ void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval,
+ const gsl_matrix *UtW, const gsl_vector *Uty,
+ const gsl_matrix *W, const gsl_vector *y);
+ // WJA added.
+ void Analyzebgen (const gsl_matrix *U, const gsl_vector *eval,
+ const gsl_matrix *UtW, const gsl_vector *Uty,
+ const gsl_matrix *W, const gsl_vector *y);
+ void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval,
+ const gsl_matrix *UtW, const gsl_vector *Uty,
+ const gsl_matrix *W, const gsl_vector *y);
+ void AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval,
+ const gsl_matrix *UtW, const gsl_vector *Uty,
+ const gsl_matrix *W, const gsl_vector *y,
+ const gsl_vector *env);
+ void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval,
+ const gsl_matrix *UtW, const gsl_vector *Uty,
+ const gsl_matrix *W, const gsl_vector *y,
+ const gsl_vector *env);
void WriteFiles ();
- void CalcRLWald (const double &lambda, const FUNC_PARAM &params, double &beta, double &se, double &p_wald);
- void CalcRLScore (const double &l, const FUNC_PARAM &params, double &beta, double &se, double &p_score);
+ void CalcRLWald (const double &lambda, const FUNC_PARAM &params,
+ double &beta, double &se, double &p_wald);
+ void CalcRLScore (const double &l, const FUNC_PARAM &params,
+ double &beta, double &se, double &p_score);
};
-void MatrixCalcLR (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const double l_min, const double l_max, const size_t n_region, vector<pair<size_t, double> > &pos_loglr);
-void CalcLambda (const char func_name, FUNC_PARAM &params, const double l_min, const double l_max, const size_t n_region, double &lambda, double &logf);
-void CalcLambda (const char func_name, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double l_min, const double l_max, const size_t n_region, double &lambda, double &logl_H0);
-void CalcPve (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double lambda, const double trace_G, double &pve, double &pve_se);
-void CalcLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double lambda, double &vg, double &ve, gsl_vector *beta, gsl_vector *se_beta);
+void MatrixCalcLR (const gsl_matrix *U, const gsl_matrix *UtX,
+ const gsl_vector *Uty, const gsl_vector *K_eval,
+ const double l_min, const double l_max,
+ const size_t n_region,
+ vector<pair<size_t, double> > &pos_loglr);
+void CalcLambda (const char func_name, FUNC_PARAM &params,
+ const double l_min, const double l_max,
+ const size_t n_region, double &lambda, double &logf);
+void CalcLambda (const char func_name, const gsl_vector *eval,
+ const gsl_matrix *UtW, const gsl_vector *Uty,
+ const double l_min, const double l_max,
+ const size_t n_region, double &lambda, double &logl_H0);
+void CalcPve (const gsl_vector *eval, const gsl_matrix *UtW,
+ const gsl_vector *Uty, const double lambda,
+ const double trace_G, double &pve, double &pve_se);
+void CalcLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW,
+ const gsl_vector *Uty, const double lambda, double &vg,
+ double &ve, gsl_vector *beta, gsl_vector *se_beta);
#endif
diff --git a/src/logistic.cpp b/src/logistic.cpp
index 002ce98..3f9d6ff 100644
--- a/src/logistic.cpp
+++ b/src/logistic.cpp
@@ -13,7 +13,7 @@ typedef struct{
gsl_matrix_int *X;
gsl_vector_int *nlev;
gsl_vector *y;
- gsl_matrix *Xc; // continuous covariates matrix Nobs x Kc (NULL if not used)
+ gsl_matrix *Xc; // Continuous covariates matrix Nobs x Kc (NULL if not used).
double lambdaL1;
double lambdaL2;
} fix_parm_mixed_T;
@@ -29,8 +29,9 @@ double fLogit_mixed(gsl_vector *beta,
int npar = beta->size;
double total = 0;
double aux = 0;
+
// Changed loop start at 1 instead of 0 to avoid regularization of
- // beta_0*\/ */
+ // beta_0*\/
// #pragma omp parallel for reduction (+:total)
for(int i = 1; i < npar; ++i)
total += beta->data[i]*beta->data[i];
@@ -57,8 +58,9 @@ double fLogit_mixed(gsl_vector *beta,
}
-void logistic_mixed_pred(gsl_vector *beta // Vector of parameters length = 1 + Sum_k(C_k - 1)
- ,gsl_matrix_int *X //Matrix Nobs x K
+void logistic_mixed_pred(gsl_vector *beta // Vector of parameters
+ // length = 1 + Sum_k(C_k -1)
+ ,gsl_matrix_int *X //Matrix Nobs x K
,gsl_vector_int *nlev // Vector with number categories
,gsl_matrix *Xc // continuous covariates Matrix Nobs x Kc (NULL if not used)
,gsl_vector *yhat //Vector of prob. predicted by the logistic
@@ -287,39 +289,40 @@ int logistic_mixed_fit(gsl_vector *beta
/* Categorical */
/***************/
-// I need to bundle all the data that goes to the function to optimze together.
+// I need to bundle all the data that goes to the function to optimze
+// together.
typedef struct{
gsl_matrix_int *X;
gsl_vector_int *nlev;
gsl_vector *y;
double lambdaL1;
double lambdaL2;
-}fix_parm_cat_T;
-
-
-double fLogit_cat(gsl_vector *beta
- ,gsl_matrix_int *X
- ,gsl_vector_int *nlev
- ,gsl_vector *y
- ,double lambdaL1
- ,double lambdaL2)
-{
+} fix_parm_cat_T;
+
+double fLogit_cat(gsl_vector *beta,
+ gsl_matrix_int *X,
+ gsl_vector_int *nlev,
+ gsl_vector *y,
+ double lambdaL1,
+ double lambdaL2) {
int n = y->size;
- // int k = X->size2;
int npar = beta->size;
double total = 0;
double aux = 0;
- /* omp_set_num_threads(ompthr); */
- /* /\* Changed loop start at 1 instead of 0 to avoid regularization of beta 0*\/ */
- /* /\*#pragma omp parallel for reduction (+:total)*\/ */
+ // omp_set_num_threads(ompthr); /\* Changed loop start at 1 instead
+ // of 0 to avoid regularization of beta 0*\/ /\*#pragma omp parallel
+ // for reduction (+:total)*\/
for(int i = 1; i < npar; ++i)
total += beta->data[i]*beta->data[i];
total = (-total*lambdaL2/2);
- /* /\*#pragma omp parallel for reduction (+:aux)*\/ */
+
+ // /\*#pragma omp parallel for reduction (+:aux)*\/
for(int i = 1; i < npar; ++i)
aux += (beta->data[i]>0 ? beta->data[i] : -beta->data[i]);
total = total-aux*lambdaL1;
- /* #pragma omp parallel for schedule(static) shared(n,beta,X,nlev,y) reduction (+:total) */
+
+ // #pragma omp parallel for schedule(static) shared(n,beta,X,nlev,y)
+ // #reduction (+:total)
for(int i = 0; i < n; ++i) {
double Xbetai=beta->data[0];
int iParm=1;
@@ -333,7 +336,6 @@ double fLogit_cat(gsl_vector *beta
return -total;
}
-
void logistic_cat_pred(gsl_vector *beta // Vector of parameters length = 1 + Sum_k(C_k - 1)
,gsl_matrix_int *X //Matrix Nobs x K
,gsl_vector_int *nlev // Vector with number categories
diff --git a/src/mvlmm.h b/src/mvlmm.h
index 9ff567c..d495c26 100644
--- a/src/mvlmm.h
+++ b/src/mvlmm.h
@@ -1,6 +1,6 @@
/*
Genome-wide Efficient Mixed Model Association (GEMMA)
- Copyright (C) 2011 Xiang Zhou
+ 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
@@ -13,36 +13,25 @@
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/>.
- */
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+*/
#ifndef __MVLMM_H__
#define __MVLMM_H__
#include "gsl/gsl_vector.h"
#include "gsl/gsl_matrix.h"
-
-
-#ifdef FORCE_FLOAT
-#include "param_float.h"
-#include "io_float.h"
-#else
#include "param.h"
#include "io.h"
-#endif
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
+ // 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;
@@ -50,48 +39,68 @@ public:
string file_out;
string path_out;
- // MVLMM related parameters
+ // 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, VVe_mle_null;
- vector<double> beta_remle_null, se_beta_remle_null, beta_mle_null, se_beta_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
+ // 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
+ 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;
- 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
+ // 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
+ vector<SNPINFO> snpInfo; // Record SNP information.
- // Not included in PARAM
- vector<MPHSUMSTAT> sumStat; //Output SNPSummary Data
+ // 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 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
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