| /dports/biology/gcta/gcta_1.26.0_src/ |
| H A D | grm.cpp | 377 void gcta::rm_cor_indi(double grm_cutoff) { in rm_cor_indi() argument
378 cout << "Pruning the GRM with a cutoff of " << grm_cutoff << " ..." << endl; in rm_cor_indi()
386 if (_grm(_keep[i], _keep[j]) > grm_cutoff) { in rm_cor_indi()
480 …tring keep_indi_file, string remove_indi_file, string sex_file, double grm_cutoff, double adj_grm_… in manipulate_grm() argument
490 if (grm_cutoff>-1.0) rm_cor_indi(grm_cutoff); in manipulate_grm()
494 if (grm_cutoff>-1.0 || !keep_indi_file.empty() || !remove_indi_file.empty()) { in manipulate_grm()
509 …tring keep_indi_file, string remove_indi_file, string sex_file, double grm_cutoff, double adj_grm_… in save_grm() argument
511 …manipulate_grm(grm_file, keep_indi_file, remove_indi_file, sex_file, grm_cutoff, adj_grm_fac, dosa… in save_grm()
608 void gcta::pca(string grm_file, string keep_indi_file, string remove_indi_file, double grm_cutoff, … in pca() argument
610 …manipulate_grm(grm_file, keep_indi_file, remove_indi_file, "", grm_cutoff, -2.0, -2, merge_grm_fla… in pca()
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| H A D | option.cpp | 70 double grm_adj_fac = -2.0, grm_cutoff = -2.0, rm_high_ld_cutoff = -1.0, bK_threshold = -10.0; in option() local
398 grm_cutoff = atof(argv[++i]); in option()
399 if (grm_cutoff >= -1 && grm_cutoff <= 2) cout << "--grm-cutoff " << grm_cutoff << endl; in option()
400 else grm_cutoff = -2; in option()
931 …if(bfile_flag && grm_cutoff>-1.0) throw ("Error: the --grm-cutoff option is invalid when used in c… in option()
937 if (grm_cutoff>-1.0) { in option()
938 grm_cutoff = -2.0; in option()
1118 …ovar_file, kp_indi_file, rm_indi_file, update_sex_file, mphen, mphen2, grm_cutoff, grm_adj_fac, do… in option()
1120 …xe_file, gxe_file, kp_indi_file, rm_indi_file, update_sex_file, mphen, grm_cutoff, grm_adj_fac, do… in option()
1122 …if (pca_flag) pter_gcta->pca(grm_file, kp_indi_file, rm_indi_file, grm_cutoff, m_grm_flag, out_pc_… in option()
[all …]
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| H A D | gcta.h | 101 …tring keep_indi_file, string remove_indi_file, string sex_file, double grm_cutoff, double adj_grm_…
102 …void pca(string grm_file, string keep_indi_file, string remove_indi_file, double grm_cutoff, bool …
109 …indi_file, string remove_indi_file, string sex_file, int mphen, double grm_cutoff, double adj_grm_…
120 …tring remove_indi_file, string sex_file, int mphen, int mphen2, double grm_cutoff, double adj_grm_…
225 void rm_cor_indi(double grm_cutoff);
228 …tring keep_indi_file, string remove_indi_file, string sex_file, double grm_cutoff, double adj_grm_…
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| H A D | bivar_reml.cpp | 15 …tring remove_indi_file, string sex_file, int mphen, int mphen2, double grm_cutoff, double adj_grm_… in fit_bivar_reml() argument
59 if (grm_cutoff>-1.0) rm_cor_indi(grm_cutoff); in fit_bivar_reml()
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| H A D | est_hsq.cpp | 171 …indi_file, string remove_indi_file, string sex_file, int mphen, double grm_cutoff, double adj_grm_… in fit_reml() argument
225 if (grm_cutoff>-1.0) rm_cor_indi(grm_cutoff); in fit_reml()
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