/dports/biology/gemma/GEMMA-0.98.3/src/ |
H A D | prdt.cpp | 53 indicator_idv = cPar.indicator_idv; in CopyFromParam() 91 if (indicator_idv[i] == 1) { in WriteFiles() 146 gsl_vector_set(w, i, indicator_idv[i]); in AddBV() 157 if (indicator_idv[i] == 1 && indicator_idv[j] == 1) { in AddBV() 160 if (indicator_idv[i] == 0 && indicator_idv[j] == 1) { in AddBV() 163 if (indicator_idv[j] == 1) { in AddBV() 167 if (indicator_idv[i] == 1) { in AddBV() 255 if (indicator_idv[i] == 1) { in AnalyzeBimbam() 329 if (indicator_idv.size() % 4 == 0) { in AnalyzePlink() 330 n_bit = indicator_idv.size() / 4; in AnalyzePlink() [all …]
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H A D | gemma_io.h | 63 const gsl_matrix *W, vector<int> &indicator_idv, 71 const gsl_matrix *W, vector<int> &indicator_idv, 78 void Plink_ReadOneSNP(const int pos, const vector<int> &indicator_idv, 81 void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv, 84 void ReadFile_mk(const string &file_mk, vector<int> &indicator_idv, 97 bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv, 100 bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv, 108 bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv, 134 const vector<int> &indicator_idv, 141 const vector<int> &indicator_idv, [all …]
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H A D | param.cpp | 214 indicator_idv.push_back(k); in ReadFiles() 454 indicator_idv.push_back(k); in ReadFiles() 479 ni_test += indicator_idv[i]; in ReadFiles() 1035 if (indicator_idv[i] == 0) { in CheckData() 1148 if (indicator_idv[i] == 0) { in CheckData() 1995 indicator_idv.clear(); in ProcessCvtPhen() 2003 indicator_idv.push_back(k); in ProcessCvtPhen() 2030 if (indicator_idv[i] == 0) { in ProcessCvtPhen() 2063 indicator_idv[i] = 0; in ProcessCvtPhen() 2149 if (indicator_idv[i] == 0) { in CopyCvtPhen() [all …]
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H A D | vc.h | 100 vector<int> &indicator_idv, vector<int> &indicator_snp, 104 vector<int> &indicator_idv, vector<int> &indicator_snp, 108 const int display_pace, vector<int> &indicator_idv, 114 vector<int> &indicator_idv, vector<int> &indicator_snp, 117 vector<int> &indicator_idv, vector<int> &indicator_snp, 120 const int display_pace, vector<int> &indicator_idv,
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H A D | varcov.cpp | 62 indicator_idv = cPar.indicator_idv; in CopyFromParam() 262 for (size_t i = 0; i < indicator_idv.size(); i++) { in AnalyzeBimbam() 263 ni_test += indicator_idv[i]; in AnalyzeBimbam() 307 Bimbam_ReadOneSNP(inc, indicator_idv, infile, geno, geno_mean); in AnalyzeBimbam() 362 for (size_t i = 0; i < indicator_idv.size(); i++) { in AnalyzePlink() 363 ni_test += indicator_idv[i]; in AnalyzePlink() 407 Plink_ReadOneSNP(t2, indicator_idv, infile, geno, geno_mean); in AnalyzePlink()
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H A D | ldr.cpp | 64 indicator_idv = cPar.indicator_idv; in CopyFromParam()
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H A D | gemma_io.cpp | 343 indicator_idv.clear(); in ReadFile_column() 365 indicator_idv.push_back(0); in ReadFile_column() 370 indicator_idv.push_back(1); in ReadFile_column() 689 ni_test += indicator_idv[i]; in ReadFile_geno() 745 if (indicator_idv[i] == 0) in ReadFile_geno() 897 ni_test += indicator_idv[i]; in ReadFile_bed() 1077 if (indicator_idv[i] == 0) { in Bimbam_ReadOneSNP() 1133 if (indicator_idv[c] == 0) { in Plink_ReadOneSNP() 1231 if (indicator_idv[i] == 1) { in ReadFile_kin() 1771 if (indicator_idv[j] == 0) { in ReadFile_geno() [all …]
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H A D | lm.cpp | 70 indicator_idv = cPar.indicator_idv; in CopyFromParam() 340 for (size_t i = 0; i < indicator_idv.size(); ++i) { in AnalyzeGene() 342 if (indicator_idv[i] == 0) { in AnalyzeGene() 440 if (indicator_idv[i] == 0) { in AnalyzeBimbam() 573 if (indicator_idv[ci_total] == 0) { in AnalyzePlink()
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H A D | ldr.h | 50 vector<int> indicator_idv; variable
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H A D | varcov.h | 39 vector<int> indicator_idv; variable
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H A D | prdt.h | 45 vector<int> indicator_idv; variable
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H A D | lm.h | 53 vector<int> indicator_idv; variable
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H A D | vc.cpp | 2263 for (size_t i = 0; i < indicator_idv.size(); ++i) { in BimbamXwz() 2264 if (indicator_idv[i] == 0) { in BimbamXwz() 2315 vector<int> &indicator_idv, vector<int> &indicator_snp, in PlinkXwz() argument 2332 size_t ni_total = indicator_idv.size(); in PlinkXwz() 2379 if (indicator_idv[ci_total] == 0) { in PlinkXwz() 2441 const int display_pace, vector<int> &indicator_idv, in MFILEXwz() argument 2516 for (size_t i = 0; i < indicator_idv.size(); ++i) { in BimbamXtXwz() 2517 if (indicator_idv[i] == 0) { in BimbamXtXwz() 2585 size_t ni_total = indicator_idv.size(); in PlinkXtXwz() 2629 if (indicator_idv[ci_total] == 0) { in PlinkXtXwz() [all …]
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H A D | gemma.cpp | 1678 for (size_t i = 0; i < cPar.indicator_idv.size(); i++) { in BatchRun() 2328 ReadFile_mk(cPar.file_mk, cPar.indicator_idv, cPar.mapID2num, in BatchRun() 2483 BimbamXwz(cPar.file_geno, cPar.d_pace, cPar.indicator_idv, in BatchRun() 2486 MFILEXwz(1, cPar.file_mbfile, cPar.d_pace, cPar.indicator_idv, in BatchRun() 2489 MFILEXwz(0, cPar.file_mgeno, cPar.d_pace, cPar.indicator_idv, in BatchRun() 2504 BimbamXwz(cPar.file_geno, cPar.d_pace, cPar.indicator_idv, in BatchRun() 2507 MFILEXwz(1, cPar.file_mbfile, cPar.d_pace, cPar.indicator_idv, in BatchRun() 2510 MFILEXwz(0, cPar.file_mgeno, cPar.d_pace, cPar.indicator_idv, in BatchRun() 2523 BimbamXtXwz(cPar.file_geno, cPar.d_pace, cPar.indicator_idv, in BatchRun() 2529 MFILEXtXwz(0, cPar.file_mgeno, cPar.d_pace, cPar.indicator_idv, in BatchRun() [all …]
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H A D | mvlmm.h | 67 vector<int> indicator_idv; variable
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H A D | bslmmdap.h | 68 vector<int> indicator_idv; variable
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H A D | lmm.h | 80 vector<int> indicator_idv; variable
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H A D | bslmm.h | 82 vector<int> indicator_idv; variable
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H A D | lmm.cpp | 81 indicator_idv = cPar.indicator_idv; in CopyFromParam() 1397 for (size_t i = 0; i < indicator_idv.size(); ++i) { in AnalyzeGene() 1399 if (indicator_idv[i] == 0) { in AnalyzeGene() 1584 if (indicator_idv[i] == 0) // skip individual in Analyze() 1780 if (indicator_idv[ci_total] == 0) { in AnalyzePlink() 2287 if (indicator_idv[i] == 0) { in AnalyzeBimbamGXE() 2454 if (indicator_idv[ci_total] == 0) { in AnalyzePlinkGXE()
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H A D | param.h | 283 vector<int> indicator_idv; variable
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H A D | bslmmdap.cpp | 86 indicator_idv = cPar.indicator_idv; in CopyFromParam()
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H A D | bslmm.cpp | 97 indicator_idv = cPar.indicator_idv; in CopyFromParam() 129 if (indicator_idv[i] == 0) { in WriteBV()
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H A D | mvlmm.cpp | 86 indicator_idv = cPar.indicator_idv; in CopyFromParam() 3228 if (indicator_idv[i] == 0) { in AnalyzeBimbam() 3693 if (indicator_idv[ci_total] == 0) { in AnalyzePlink() 4214 if (indicator_idv[i] == 0) { in AnalyzeBimbamGXE() 4679 if (indicator_idv[ci_total] == 0) { in AnalyzePlinkGXE()
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