| /dports/biology/gcta/gcta_1.26.0_src/ |
| H A D | option.cpp | 100 …string phen_file = "", qcovar_file = "", covar_file = "", qgxe_file = "", gxe_file = "", blup_indi… in option() local
643 phen_file = argv[++i]; in option()
644 cout << "--pheno " << phen_file << endl; in option()
645 CommFunc::FileExist(phen_file); in option()
1064 …else if (mlma_flag) pter_gcta->mlma(grm_file, m_grm_flag, subtract_grm_file, phen_file, qcovar_fil… in option()
1065 …else if (mlma_loco_flag) pter_gcta->mlma_loco(phen_file, qcovar_file, covar_file, mphen, MaxIter, … in option()
1113 …else if (mlma_flag) pter_gcta->mlma(grm_file, m_grm_flag, subtract_grm_file, phen_file, qcovar_fil… in option()
1114 …else if (mlma_loco_flag) pter_gcta->mlma_loco(phen_file, qcovar_file, covar_file, mphen, MaxIter, … in option()
1115 … } else if (HE_reg_flag) pter_gcta->HE_reg(grm_file, phen_file, kp_indi_file, rm_indi_file, mphen); in option()
1116 …else if ((reml_flag || bivar_reml_flag) && phen_file.empty()) throw ("\nError: phenotype file is r… in option()
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| H A D | est_hsq.cpp | 40 void gcta::read_phen(string phen_file, vector<string> &phen_ID, vector< vector<string> > &phen_buf,… in read_phen() argument
42 ifstream in_phen(phen_file.c_str()); in read_phen()
43 if (!in_phen) throw ("Error: can not open the file [" + phen_file + "] to read."); in read_phen()
50 cout << "Reading phenotypes from [" + phen_file + "]." << endl; in read_phen()
54 …) cout << "There are " << phen_num << " traits specified in the file [" + phen_file + "]." << endl; in read_phen()
57 … errmsg << "Error: can not find the " << mphen << "th trait in the file [" + phen_file + "]."; in read_phen()
62 … errmsg << "Error: can not find the " << mphen2 << "th trait in the file [" + phen_file + "]."; in read_phen()
95 …henotypes of " << phen_buf.size() << " individuals are included from [" + phen_file + "]." << endl; in read_phen()
202 read_phen(phen_file, phen_ID, phen_buf, mphen); in fit_reml()
1483 void gcta::HE_reg(string grm_file, string phen_file, string keep_indi_file, string remove_indi_file… in HE_reg() argument
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| H A D | gcta.h | 109 …void fit_reml(string grm_file, string phen_file, string qcovar_file, string covar_file, string qGE…
110 …void HE_reg(string grm_file, string phen_file, string keep_indi_file, string remove_indi_file, int…
120 …void fit_bivar_reml(string grm_file, string phen_file, string qcovar_file, string covar_file, stri…
157 …void mlma(string grm_file, bool m_grm_flag, string subtract_grm_file, string phen_file, string qco…
158 …void mlma_loco(string phen_file, string qcovar_file, string covar_file, int mphen, int MaxIter, ve…
233 …void read_phen(string phen_file, vector<string> &phen_ID, vector< vector<string> > &phen_buf, int …
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| H A D | mlm_assoc.cpp | 15 void gcta::mlma(string grm_file, bool m_grm_flag, string subtract_grm_file, string phen_file, strin… in mlma() argument
34 read_phen(phen_file, phen_ID, phen_buf, mphen); in mlma()
346 void gcta::mlma_loco(string phen_file, string qcovar_file, string covar_file, int mphen, int MaxIte… in mlma_loco() argument
359 read_phen(phen_file, phen_ID, phen_buf, mphen); in mlma_loco()
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| H A D | bivar_reml.cpp | 15 void gcta::fit_bivar_reml(string grm_file, string phen_file, string qcovar_file, string covar_file,… in fit_bivar_reml() argument
46 read_phen(phen_file, phen_ID, phen_buf, mphen, mphen2); in fit_bivar_reml()
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