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Searched refs:indicator_idv (Results 1 – 23 of 23) sorted by relevance

/dports/biology/gemma/GEMMA-0.98.3/src/
H A Dprdt.cpp53 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()
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H A Dgemma_io.h63 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,
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H A Dparam.cpp214 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()
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H A Dvc.h100 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,
H A Dvarcov.cpp62 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()
H A Dldr.cpp64 indicator_idv = cPar.indicator_idv; in CopyFromParam()
H A Dgemma_io.cpp343 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()
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H A Dlm.cpp70 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()
H A Dldr.h50 vector<int> indicator_idv; variable
H A Dvarcov.h39 vector<int> indicator_idv; variable
H A Dprdt.h45 vector<int> indicator_idv; variable
H A Dlm.h53 vector<int> indicator_idv; variable
H A Dvc.cpp2263 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()
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H A Dgemma.cpp1678 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()
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H A Dmvlmm.h67 vector<int> indicator_idv; variable
H A Dbslmmdap.h68 vector<int> indicator_idv; variable
H A Dlmm.h80 vector<int> indicator_idv; variable
H A Dbslmm.h82 vector<int> indicator_idv; variable
H A Dlmm.cpp81 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()
H A Dparam.h283 vector<int> indicator_idv; variable
H A Dbslmmdap.cpp86 indicator_idv = cPar.indicator_idv; in CopyFromParam()
H A Dbslmm.cpp97 indicator_idv = cPar.indicator_idv; in CopyFromParam()
129 if (indicator_idv[i] == 0) { in WriteBV()
H A Dmvlmm.cpp86 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()