| /dports/biology/gcta/gcta_1.26.0_src/ |
| H A D | mlm_assoc.cpp | 15 …string subtract_grm_file, string phen_file, string qcovar_file, string covar_file, int mphen, int … in mlma() argument
22 bool covar_flag=(!covar_file.empty()); in mlma()
41 covar_num=read_covar(covar_file, covar_ID, covar, false); in mlma()
346 void gcta::mlma_loco(string phen_file, string qcovar_file, string covar_file, int mphen, int MaxIte… in mlma_loco() argument
351 bool covar_flag=(!covar_file.empty()); in mlma_loco()
366 covar_num=read_covar(covar_file, covar_ID, covar, false); in mlma_loco()
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| H A D | option.cpp | 100 …string phen_file = "", qcovar_file = "", covar_file = "", qgxe_file = "", gxe_file = "", blup_indi… in option() local
655 covar_file = argv[++i]; in option()
656 cout << "--covar " << covar_file << endl; in option()
657 CommFunc::FileExist(covar_file); in option()
1064 …>mlma(grm_file, m_grm_flag, subtract_grm_file, phen_file, qcovar_file, covar_file, mphen, MaxIter,… in option()
1065 …else if (mlma_loco_flag) pter_gcta->mlma_loco(phen_file, qcovar_file, covar_file, mphen, MaxIter, … in option()
1113 …>mlma(grm_file, m_grm_flag, subtract_grm_file, phen_file, qcovar_file, covar_file, mphen, MaxIter,… in option()
1114 …else if (mlma_loco_flag) pter_gcta->mlma_loco(phen_file, qcovar_file, covar_file, mphen, MaxIter, … in option()
1118 …pter_gcta->fit_bivar_reml(grm_file, phen_file, qcovar_file, covar_file, kp_indi_file, rm_indi_file… in option()
1120 …pter_gcta->fit_reml(grm_file, phen_file, qcovar_file, covar_file, qgxe_file, gxe_file, kp_indi_fil… in option()
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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…
120 …void fit_bivar_reml(string grm_file, string phen_file, string qcovar_file, string covar_file, stri…
157 …string subtract_grm_file, string phen_file, string qcovar_file, string covar_file, int mphen, int …
158 …void mlma_loco(string phen_file, string qcovar_file, string covar_file, int mphen, int MaxIter, ve…
235 …int read_covar(string covar_file, vector<string> &covar_ID, vector< vector<string> > &covar, bool …
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| H A D | est_hsq.cpp | 105 int gcta::read_covar(string covar_file, vector<string> &covar_ID, vector< vector<string> > &covar, … in read_covar() argument
107 ifstream in_covar(covar_file.c_str()); in read_covar()
108 if (!in_covar) throw ("Error: can not open the file [" + covar_file + "] to read."); in read_covar()
115 if (qcovar_flag) cout << "Reading quantitative covariates from [" + covar_file + "]." << endl; in read_covar()
116 else cout << "Reading discrete covariate(s) from [" + covar_file + "]." << endl; in read_covar()
118 …ive covariate(s) of " << covar_ID.size() << " individuals read from [" + covar_file + "]." << endl; in read_covar()
119 …riate(s) of " << covar_ID.size() << " individuals are included from [" + covar_file + "]." << endl; in read_covar()
171 void gcta::fit_reml(string grm_file, string phen_file, string qcovar_file, string covar_file, strin… in fit_reml() argument
179 bool covar_flag = (!covar_file.empty()); in fit_reml()
209 covar_num = read_covar(covar_file, covar_ID, covar, false); in fit_reml()
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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
25 bool covar_flag = (!covar_file.empty()); in fit_bivar_reml()
53 covar_num = read_covar(covar_file, covar_ID, covar, false); in fit_bivar_reml()
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| /dports/biology/plink/plink-ng-79b2df8c/1.9/ |
| H A D | plink_data.c | 1204 FILE* covar_file = nullptr; in load_covars() local
1297 if (fopen_checked(covar_fname, "r", &covar_file)) { in load_covars()
1302 if (!fgets(loadbuf, loadbuf_size, covar_file)) { in load_covars()
1303 if (!feof(covar_file)) { in load_covars()
1441 rewind(covar_file); in load_covars()
1452 …retval = load_to_first_token(covar_file, loadbuf_size, '\0', "--covar file", loadbuf, &bufptr, &li… in load_covars()
1471 while (fgets(loadbuf, loadbuf_size, covar_file)) { in load_covars()
1568 if (!feof(covar_file)) { in load_covars()
1703 fclose_cond(covar_file); in load_covars()
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