Searched refs:_snp_name (Results 1 – 15 of 15) sorted by relevance
28 _snp_name.push_back(vs_buf[++j]); in read_IRG_fnames()33 _snp_num=_snp_name.size(); in read_IRG_fnames()41 for(i=0; i<_snp_num; i++) omap<<_chr[i]<<"\t"<<_snp_name[i]<<"\t0\t"<<_bp[i]<<endl; in read_IRG_fnames()106 …if(vs_buf[0]!=_snp_name[i]) throw("Error: the SNP ["+vs_buf[0]+"] specified in the summary file do… in read_one_IRG()
147 _snp_name.clear(); in read_bimfile()157 _snp_name.push_back(str_buf); in read_bimfile()191 _snp_name[i] = ss.str(); in init_include()295 _snp_name.clear(); in update_bim()304 _snp_name = snp_name_buf; in update_bim()379 _snp_name.clear(); in read_imp_info_mach_gz()388 _snp_name.push_back(str_buf); in read_imp_info_mach_gz()399 _snp_num = _snp_name.size(); in read_imp_info_mach_gz()429 _snp_name.clear(); in read_imp_info_mach()446 _snp_num = _snp_name.size(); in read_imp_info_mach()[all …]
150 str_buf=plk->_snp_name[plk->_include[i]]; in grm_between()162 if(_snp_name[_include[i]]!=plk->_snp_name[plk->_include[i]]){ in grm_between()163 …<" th SNP included in the analysis is "<<_snp_name[_include[i]]<<" in the first dataset but is "<<… in grm_between()167 …errmsg<<"Error: the reference allele for the SNP "<<_snp_name[_include[i]]<<" is "<<_ref_A[_includ… in grm_between()
28 for (i = 0; i < _snp_num; i++) snp_map_buf.insert(pair<string, int>(_snp_name[i], i)); in read_LD_target_SNPs()49 for (i = 0; i < _include.size(); i++) uni_snp.push_back(_snp_name[_include[i]]); in LD_Blocks()156 L_SNP[i] = _snp_name[_include[maxL]]; in EstLD()157 R_SNP[i] = _snp_name[_include[maxR]]; in EstLD()160 snp[i].push_back(_snp_name[_include[buf[j]]]); in EstLD()296 … o_mrsq << _snp_name[_include[i]] << " " << _chr[_include[i]] << " " << _bp[_include[i]] << " "; in calcu_mean_rsq()538 for (i = 0; i < m; i++) snp_map.insert(pair<string, int>(_snp_name[_include[i]], i)); in calcu_mean_rsq_multiSet()575 … o_mrsq << _snp_name[_include[i]] << " " << _chr[_include[i]] << " " << _bp[_include[i]] << " "; in calcu_mean_rsq_multiSet()762 _snp_name.resize(m); in ld_seg()775 _snp_name[i] = str_buf; in ld_seg()[all …]
34 _snp_name.clear(); in read_imp_info_mach()44 _snp_name.push_back(str_buf); in read_imp_info_mach()55 _snp_num=_snp_name.size(); in read_imp_info_mach()
57 bad_snp.push_back(_snp_name[i]); in read_metafile()92 iter = id_map.find(_snp_name[_include[i]]); in read_metafile()163 if (givenSNPs_map.find(_snp_name[_include[i]]) != givenSNPs_map.end()) pgiven.push_back(i); in read_fixed_snp()245 …ofile << _chr[_include[j]] << "\t" << _snp_name[_include[j]] << "\t" << _bp[_include[j]] << "\t" <… in run_massoc_cond()264 … ofile << _chr[_include[j]] << "\t" << _snp_name[_include[j]] << "\t" << _bp[_include[j]] << "\t"; in massoc_slct_output()278 for (i = 0; i < slct.size(); i++) ofile << _snp_name[_include[slct[i]]] << "\t"; in massoc_slct_output()281 ofile << _snp_name[_include[slct[i]]] << "\t"; in massoc_slct_output()298 … ofile << _chr[_include[j]] << "\t" << _snp_name[_include[j]] << "\t" << _bp[_include[j]] << "\t"; in massoc_cond_output()719 …ofile << _snp_name[_include[j]] << "\t" << _ref_A[_include[j]] << "\t" << _beta[j] << "\t" << bJ[j… in run_massoc_sblup()
122 for (i = 0; i < qtl_num; i++) vs_buf[i] = _snp_name[_include[i]]; in GWAS_simu()500 int snp_num = _snp_name.size(); in genet_dst()555 …for (i = 0; i < snp_num; i++) out_bim << _chr[i] << "\t" << _snp_name[i] << "\t" << dst[i]*1e-6 <<… in genet_dst()
513 for (i = 0; i < m_sub; i++) rm_snp_name[i] = _snp_name[_include[rm_snp_indx[i]]]; in LD_pruning_mkl()520 for (i = 0; i < m; i++) oprune << _snp_name[_include[i]] << endl; in LD_pruning_mkl()582 …for (i = 0; i < m; i++) o_mrsq << _snp_name[_include[i]] << " " << 0.5 * _mu[_include[i]] << " " <… in calcu_mean_rsq_mkl()
228 ofile<<_chr[j]<<"\t"<<_snp_name[j]<<"\t"<<_bp[j]<<"\t"<<_ref_A[j]<<"\t"<<_other_A[j]<<"\t"; in mlma()501 … ofile<<_chr[j]<<"\t"<<_snp_name[j]<<"\t"<<_bp[j]<<"\t"<<_ref_A[j]<<"\t"<<_other_A[j]<<"\t"; in mlma_loco()
46 map<string, int>::iterator iter = snp_name_buf_map.find(_snp_name[_include[i]]); in gbat_read_snpAssoc()
236 …ofile<<_chr[_include[i]]<<"\t"<<_snp_name[_include[i]]<<"\t"<<_bp[_include[i]]<<"\t"<<_ref_A[_incl… in Fst()
51 map<string, int>::iterator iter = snp_name_buf_map.find(_snp_name[_include[i]]); in sbat_read_snpAssoc()
418 vector<string> _snp_name; variable
710 ofile << _snp_name[_include[i]] << "\t" << _ref_A[_include[i]]; in snp_pc_loading()
1475 o_b_snp << _snp_name[_include[i]] << "\t" << _ref_A[_include[i]] << "\t"; in output_blup_snp()