| /dports/biology/gcta/gcta_1.26.0_src/ |
| H A D | grm.cpp | 189 string grm_file; in output_grm() local
192 grm_file = _out + ".grm.bin"; in output_grm()
193 fstream A_Bin(grm_file.c_str(), ios::out | ios::binary); in output_grm()
222 grm_file = _out + ".grm.gz"; in output_grm()
224 zoutf.open(grm_file.c_str()); in output_grm()
254 string grm_id_file = grm_file + ".grm.id"; in read_grm_id()
298 string grm_gzfile = grm_file + ".grm.gz", str_buf; in read_grm_gz()
342 string grm_binfile = grm_file + ".grm.bin"; in read_grm_bin()
358 string grm_Nfile = grm_file + ".grm.N.bin"; in read_grm_bin()
485 if (merge_grm_flag) merge_grm(grm_file); in manipulate_grm()
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| H A D | UnusedCode.cpp | 223 string grm_file; in grm_between() local
226 grm_file=_out+".grm.bin"; in grm_between()
227 fstream A_Bin(grm_file.c_str(), ios::out|ios::binary); in grm_between()
228 if(!A_Bin) throw("Error: can not open the file ["+grm_file+"] to write."); in grm_between()
233 …>_keep.size()<<" individuals in dataset 2 has been saved in the file ["+grm_file+"] (in binary for… in grm_between()
236 grm_file=_out+".grm.gz"; in grm_between()
238 zoutf.open( grm_file.c_str() ); in grm_between()
239 if(!zoutf.is_open()) throw("Error: can not open the file ["+grm_file+"] to write."); in grm_between()
240 …cout<<"Saving the genetic relationship matrix to the file ["+grm_file+"] (in compressed text forma… in grm_between()
245 …>_keep.size()<<" individuals in dataset 2 has been saved in the file ["+grm_file+"] (in compressed… in grm_between()
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| H A D | gcta.h | 101 …void save_grm(string grm_file, string keep_indi_file, string remove_indi_file, string sex_file, do…
102 …void pca(string grm_file, string keep_indi_file, string remove_indi_file, double grm_cutoff, bool …
106 …void grm_bK(string grm_file, string keep_indi_file, string remove_indi_file, double threshold, boo…
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…
219 int read_grm_id(string grm_file, vector<string> &grm_id, bool out_id_log, bool read_id_only);
220 …void read_grm(string grm_file, vector<string> &grm_id, bool out_id_log = true, bool read_id_only =…
221 …void read_grm_gz(string grm_file, vector<string> &grm_id, bool out_id_log = true, bool read_id_onl…
222 …void read_grm_bin(string grm_file, vector<string> &grm_id, bool out_id_log = true, bool read_id_on…
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| H A D | option.cpp | 72 string grm_file = "", paa_file = "", pc_file = ""; in option() local
309 grm_file = argv[++i]; in option()
310 cout << argv[i - 1] << " " << grm_file << endl; in option()
315 grm_file = argv[++i]; in option()
316 cout << "--mgrm-gz " << grm_file << endl; in option()
319 grm_file = argv[++i]; in option()
320 cout << argv[i - 1] << " " << grm_file << endl; in option()
325 grm_file = argv[++i]; in option()
326 cout << "--grm-gz " << grm_file << endl; 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()
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| H A D | mkl.cpp | 294 string grm_file; in output_grm_mkl() local
298 grm_file = _out + ".grm.bin"; in output_grm_mkl()
299 fstream A_Bin(grm_file.c_str(), ios::out | ios::binary); in output_grm_mkl()
300 if (!A_Bin) throw ("Error: can not open the file [" + grm_file + "] to write."); in output_grm_mkl()
306 …cout << "GRM of " << n << " individuals has been saved in the file [" + grm_file + "] (in binary f… in output_grm_mkl()
319 grm_file = _out + ".grm.gz"; in output_grm_mkl()
321 zoutf.open(grm_file.c_str()); in output_grm_mkl()
322 if (!zoutf.is_open()) throw ("Error: can not open the file [" + grm_file + "] to write."); in output_grm_mkl()
323 …cout << "Saving the genetic relationship matrix to the file [" + grm_file + "] (in compressed text… in output_grm_mkl()
330 …cout << "The genetic relationship matrix has been saved in the file [" + grm_file + "] (in compres… in output_grm_mkl()
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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
20 bool grm_flag=(!grm_file.empty()); in mlma()
45 grm_files.push_back(grm_file); in mlma()
54 grm_files.push_back(grm_file); in mlma()
55 read_grm(grm_file, grm_id, true, false, true); in mlma()
59 read_grm_filenames(grm_file, grm_files, false); in mlma()
144 …e are " << grm_files.size() << " GRM file names specified in the file [" + grm_file + "]." << endl; in mlma()
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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
23 bool grm_flag = (!grm_file.empty()); in fit_bivar_reml()
35 read_grm(grm_file, grm_id, true, false, !(adj_grm_fac > -1.0)); in fit_bivar_reml()
37 grm_files.push_back(grm_file); in fit_bivar_reml()
40 read_grm_filenames(grm_file, grm_files, false); in fit_bivar_reml()
185 …e are " << grm_files.size() << " GRM file names specified in the file [" + grm_file + "]." << endl; in fit_bivar_reml()
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| H A D | est_hsq.cpp | 171 void gcta::fit_reml(string grm_file, string phen_file, string qcovar_file, string covar_file, strin… in fit_reml() argument
177 bool grm_flag = (!grm_file.empty()); in fit_reml()
191 read_grm(grm_file, grm_id, true, false, !(adj_grm_fac > -1.0)); in fit_reml()
193 grm_files.push_back(grm_file); in fit_reml()
196 read_grm_filenames(grm_file, grm_files, false); in fit_reml()
299 …e are " << grm_files.size() << " GRM file names specified in the file [" + grm_file + "]." << endl; 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
1489 read_grm(grm_file, grm_id, true, false, true); in HE_reg()
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