Added new files shared by Xiang via email on May 4, 2017.

1 files changed, 285 insertions, 0 deletions

diff --git a/src/ldr.cpp b/src/ldr.cpp
new file mode 100644
index 0000000..e28490a
--- /dev/null
+++ b/src/ldr.cpp
@@ -0,0 +1,285 @@
+/*
+ Genome-wide Efficient Mixed Model Association (GEMMA)
+ Copyright (C) 2011  Xiang Zhou
+ 
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ 
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ 
+ You should have received a copy of the GNU General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+
+#include <iomanip>
+#include <cmath>
+#include <iostream>
+#include <stdio.h>
+#include <stdlib.h> 
+#include <ctime>
+#include <cstring>
+#include <algorithm>
+
+#include "gsl/gsl_vector.h"
+#include "gsl/gsl_matrix.h"
+#include "gsl/gsl_linalg.h"
+#include "gsl/gsl_blas.h"
+#include "gsl/gsl_eigen.h"
+#include "gsl/gsl_randist.h"
+#include "gsl/gsl_cdf.h"
+#include "gsl/gsl_roots.h"
+#include "Eigen/Dense"
+
+
+
+#include "lapack.h"
+
+#ifdef FORCE_FLOAT
+#include "param_float.h"
+#include "ldr_float.h"
+#include "lm_float.h"
+#include "mathfunc_float.h"  //for function CenterVector
+#else
+#include "param.h"
+#include "ldr.h"
+#include "lm.h"
+#include "mathfunc.h"
+#endif
+
+using namespace std;
+using namespace Eigen;
+
+
+
+void LDR::CopyFromParam (PARAM &cPar) 
+{
+	a_mode=cPar.a_mode;
+	d_pace=cPar.d_pace;
+	
+	file_bfile=cPar.file_bfile;
+	file_geno=cPar.file_geno;
+	file_out=cPar.file_out;
+	path_out=cPar.path_out;
+
+	ni_total=cPar.ni_total;
+	ns_total=cPar.ns_total;
+	ni_test=cPar.ni_test;
+	ns_test=cPar.ns_test;
+	n_cvt=cPar.n_cvt;
+	
+	indicator_idv=cPar.indicator_idv;
+	indicator_snp=cPar.indicator_snp;
+	snpInfo=cPar.snpInfo;
+	
+	return;
+}
+
+
+void LDR::CopyToParam (PARAM &cPar) 
+{
+	//cPar.pheno_mean=pheno_mean;
+	//cPar.randseed=randseed;
+	
+	return;
+}
+
+
+/*
+void BSLMM::WriteBV (const gsl_vector *bv) 
+{
+	string file_str;
+	file_str=path_out+"/"+file_out;
+	file_str+=".bv.txt";
+
+	ofstream outfile (file_str.c_str(), ofstream::out);
+	if (!outfile) {cout<<"error writing file: "<<file_str.c_str()<<endl; return;}
+	
+	size_t t=0;
+	for (size_t i=0; i<ni_total; ++i) {
+		if (indicator_idv[i]==0) {
+			outfile<<"NA"<<endl;
+		}		
+		else {
+			outfile<<scientific<<setprecision(6)<<gsl_vector_get(bv, t)<<endl;
+			t++;
+		}
+	}		
+	
+	outfile.clear();	
+	outfile.close();	
+	return;
+}
+
+
+
+
+void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector *alpha, const size_t w) 
+{
+	string file_str;
+	file_str=path_out+"/"+file_out;
+	file_str+=".param.txt";
+
+	ofstream outfile (file_str.c_str(), ofstream::out);
+	if (!outfile) {cout<<"error writing file: "<<file_str.c_str()<<endl; return;}
+	
+	outfile<<"chr"<<"\t"<<"rs"<<"\t"
+			<<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t"
+			<<"beta"<<"\t"<<"gamma"<<endl;
+	
+	size_t t=0;
+	for (size_t i=0; i<ns_total; ++i) {
+		if (indicator_snp[i]==0) {continue;}		
+		
+		outfile<<snpInfo[i].chr<<"\t"<<snpInfo[i].rs_number<<"\t"
+		<<snpInfo[i].base_position<<"\t"<<snpInfo[i].n_miss<<"\t";	
+				
+		outfile<<scientific<<setprecision(6)<<gsl_vector_get(alpha, t)<<"\t";
+		if (beta_g[t].second!=0) {
+			outfile<<beta_g[t].first/beta_g[t].second<<"\t"<<beta_g[t].second/(double)w<<endl;
+		}
+		else {
+			outfile<<0.0<<"\t"<<0.0<<endl;
+		}
+		t++;
+	}		
+	
+	outfile.clear();	
+	outfile.close();	
+	return;
+}
+
+
+void BSLMM::WriteParam (const gsl_vector *alpha) 
+{
+	string file_str;
+	file_str=path_out+"/"+file_out;
+	file_str+=".param.txt";
+
+	ofstream outfile (file_str.c_str(), ofstream::out);
+	if (!outfile) {cout<<"error writing file: "<<file_str.c_str()<<endl; return;}
+	
+	outfile<<"chr"<<"\t"<<"rs"<<"\t"
+			<<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t"
+			<<"beta"<<"\t"<<"gamma"<<endl;
+	
+	size_t t=0;
+	for (size_t i=0; i<ns_total; ++i) {
+		if (indicator_snp[i]==0) {continue;}		
+
+		outfile<<snpInfo[i].chr<<"\t"<<snpInfo[i].rs_number<<"\t"
+				<<snpInfo[i].base_position<<"\t"<<snpInfo[i].n_miss<<"\t";				
+		outfile<<scientific<<setprecision(6)<<gsl_vector_get(alpha, t)<<"\t";
+		outfile<<0.0<<"\t"<<0.0<<endl;
+		t++;
+	}		
+	
+	outfile.clear();	
+	outfile.close();	
+	return;
+}
+
+
+void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl_matrix *Result_gamma, const size_t w_col) 
+{
+	string file_gamma, file_hyp;
+	file_gamma=path_out+"/"+file_out;
+	file_gamma+=".gamma.txt";
+	file_hyp=path_out+"/"+file_out;
+	file_hyp+=".hyp.txt";
+
+	ofstream outfile_gamma, outfile_hyp;
+		
+	if (flag==0) {
+		outfile_gamma.open (file_gamma.c_str(), ofstream::out);
+		outfile_hyp.open (file_hyp.c_str(), ofstream::out);
+		if (!outfile_gamma) {cout<<"error writing file: "<<file_gamma<<endl; return;}
+		if (!outfile_hyp) {cout<<"error writing file: "<<file_hyp<<endl; return;}
+		
+		outfile_hyp<<"h \t pve \t rho \t pge \t pi \t n_gamma"<<endl;
+		
+		for (size_t i=0; i<s_max; ++i) {
+			outfile_gamma<<"s"<<i<<"\t";
+		}
+		outfile_gamma<<endl;
+	}
+	else {
+		outfile_gamma.open (file_gamma.c_str(), ofstream::app);
+		outfile_hyp.open (file_hyp.c_str(), ofstream::app);
+		if (!outfile_gamma) {cout<<"error writing file: "<<file_gamma<<endl; return;}
+		if (!outfile_hyp) {cout<<"error writing file: "<<file_hyp<<endl; return;}
+		
+		size_t w;
+		if (w_col==0) {w=w_pace;}
+		else {w=w_col;}
+		
+		for (size_t i=0; i<w; ++i) {
+			outfile_hyp<<scientific;
+			for (size_t j=0; j<4; ++j) {
+				outfile_hyp<<setprecision(6)<<gsl_matrix_get (Result_hyp, i, j)<<"\t";
+			}
+			outfile_hyp<<setprecision(6)<<exp(gsl_matrix_get (Result_hyp, i, 4))<<"\t";
+			outfile_hyp<<(int)gsl_matrix_get (Result_hyp, i, 5)<<"\t";
+			outfile_hyp<<endl;
+		}
+		
+		for (size_t i=0; i<w; ++i) {
+			for (size_t j=0; j<s_max; ++j) {
+				outfile_gamma<<(int)gsl_matrix_get (Result_gamma, i, j)<<"\t";
+			}
+			outfile_gamma<<endl;
+		}
+		
+	}
+	
+	outfile_hyp.close();
+	outfile_hyp.clear();
+	outfile_gamma.close();
+	outfile_gamma.clear();	
+	return;
+}
+
+*/
+
+//X is a p by n matrix
+void LDR::VB (const vector<vector<unsigned char> > &Xt, const gsl_matrix *W_gsl, const gsl_vector *y_gsl)
+{ 
+  //save gsl_vector and gsl_matrix into eigen library formats
+  MatrixXd W(W_gsl->size1, W_gsl->size2);
+  VectorXd y(y_gsl->size);
+  VectorXd x_col(y_gsl->size);
+
+  double d;
+  for (size_t i=0; i<W_gsl->size1; i++) {
+    d=gsl_vector_get(y_gsl, i);
+    y(i)=d;
+    for (size_t j=0; j<W_gsl->size2; j++) {
+      W(i,j)=gsl_matrix_get(W_gsl, i, j);
+    }
+  }
+
+  //initial VB values by lm
+  cout<<indicator_snp[0]<<" "<<indicator_snp[1]<<" "<<indicator_snp[2]<<endl;
+  uchar_matrix_get_row (Xt, 0, x_col);
+
+  for (size_t j=0; j<10; j++) {
+    cout<<x_col(j)<<endl;
+  }
+
+
+  //run VB iterations
+
+
+
+  //save results
+
+  return;
+}