Exemplo n.º 1
0
void gcta::blup_snp_dosage()
{
    check_autosome();

    if(_mu.empty()) calcu_mu();

    int i=0, j=0, k=0, col_num=_varcmp_Py.cols();

    // Substract each element by 2p
    for(i=0; i<_keep.size(); i++){
         for(j=0; j<_include.size(); j++) _geno_dose[i][_include[j]]-=_mu[_include[j]];
	}

	// Calcuate A matrix
	cout<<"Calculating the BLUP solution to SNP effects using imputed dosage scores ... "<<endl;
	vector<double> var_SNP(_include.size()); // variance of each SNP, 2pq
    eigenMatrix b_SNP=eigenMatrix::Zero(_include.size(), col_num); // variance of each SNP, 2pq
	for(j=0; j<_include.size(); j++){
        for(i=0; i<_keep.size(); i++) var_SNP[j]+=_geno_dose[i][_include[j]]*_geno_dose[i][_include[j]];
        var_SNP[j]/=(double)(_keep.size()-1);
        if(fabs(var_SNP[j])<1.0e-50) var_SNP[j]=0.0;
        else var_SNP[j]=1.0/var_SNP[j];
	}
	for(k=0; k<_include.size(); k++){
	    for(i=0; i<_keep.size(); i++){
            for(j=0; j<col_num; j++) b_SNP(k,j)+=_geno_dose[i][_include[k]]*_varcmp_Py(i,j);
        }
        for(j=0; j<col_num; j++) b_SNP(k,j)=b_SNP(k,j)*var_SNP[k]/(double)_include.size();
	}
	output_blup_snp(b_SNP);
}
Exemplo n.º 2
0
void gcta::read_indi_blup(string blup_indi_file)
{
    vector< vector<string> > g_buf;
	ifstream i_indi_blup(blup_indi_file.c_str());
	if(!i_indi_blup) throw("Error: can not open the file ["+blup_indi_file+"] to read.");
	string str_buf, id_buf;
	vector<string> id, vs_buf;
	int i=0, j=0, k=0, col_num=0;
	while(i_indi_blup){
	    i_indi_blup>>str_buf;
	    if(i_indi_blup.eof()) break;
		id_buf=str_buf+":";
	    i_indi_blup>>str_buf;
	    id_buf+=str_buf;
		getline(i_indi_blup, str_buf);
		col_num=StrFunc::split_string(str_buf, vs_buf);
		if(col_num<1) continue;
		id.push_back(id_buf);
		g_buf.push_back(vs_buf);
	}
	i_indi_blup.close();

	update_id_map_kp(id, _id_map, _keep);
    map<string, int> uni_id_map;
    map<string, int>::iterator iter;
	for(i=0; i<_keep.size(); i++) uni_id_map.insert(pair<string,int>(_fid[_keep[i]]+":"+_pid[_keep[i]], i));
	_varcmp_Py.setZero(_keep.size(), col_num/2);
	for(i=0; i<id.size(); i++){
	    iter=uni_id_map.find(id[i]);
	    if(iter==uni_id_map.end()) continue;
	    for(j=0, k=0; j<col_num; j+=2, k++) _varcmp_Py(iter->second,k)=atof(g_buf[i][j].c_str());
	}
	cout<<"BLUP solution to the total genetic effects for "<<_keep.size()<<" individuals have been read from ["+blup_indi_file+"]."<<endl;	
}
Exemplo n.º 3
0
// blue estimate of SNP effect
void gcta::blup_snp_geno()
{
    check_autosome();

    if(_mu.empty()) calcu_mu();

    int i=0, j=0, k=0, col_num=_varcmp_Py.cols();
    double x=0.0, fcount=0.0;

	// Calcuate A matrix
	cout<<"Calculating the BLUP solution to SNP effects ..."<<endl;
	vector<double> var_SNP(_include.size());
	eigenMatrix b_SNP=eigenMatrix::Zero(_include.size(), col_num); // variance of each SNP, 2pq
	for(j=0; j<_include.size(); j++){
        var_SNP[j]=_mu[_include[j]]*(1.0-0.5*_mu[_include[j]]);
        if(fabs(var_SNP[j])<1.0e-50) var_SNP[j]=0.0;
        else var_SNP[j]=1.0/var_SNP[j];
	}
	for(k=0; k<_include.size(); k++){
	    fcount=0.0;
        for(i=0; i<_keep.size(); i++){
            if(!_snp_1[_include[k]][i] || _snp_2[_include[k]][i]){
                if(_allele1[_include[k]]==_ref_A[_include[k]]) x=_snp_1[_include[k]][i]+_snp_2[_include[k]][i];
                else x=2.0-(_snp_1[_include[k]][i]+_snp_2[_include[k]][i]);
                x=(x-_mu[_include[k]]);
                for(j=0; j<col_num; j++) b_SNP(k,j)+=x*_varcmp_Py(i,j);
                fcount+=1.0;
            }
        }
        for(j=0; j<col_num; j++) b_SNP(k,j)=(b_SNP(k,j)*var_SNP[k]/fcount)*((double)_keep.size()/(double)_include.size());
	}
	output_blup_snp(b_SNP);
}