/dports/biology/gemma/GEMMA-0.98.3/src/ |
H A D | varcov.cpp | 63 indicator_snp = cPar.indicator_snp; in CopyFromParam() 171 if (indicator_snp[t] == 0) { in CalcNB() 182 if (t == indicator_snp.size() - 1) { in CalcNB() 190 while (t2 < indicator_snp.size() && in CalcNB() 192 indicator_snp[t2] == 0) { in CalcNB() 196 while (t2 < indicator_snp.size() && in CalcNB() 208 indicator_snp[t2] == 0) { in CalcNB() 285 if (indicator_snp[t] == 0) { in AnalyzeBimbam() 302 while (t2 < indicator_snp.size() && indicator_snp[t2] == 0) { in AnalyzeBimbam() 385 if (indicator_snp[t] == 0) { in AnalyzePlink() [all …]
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H A D | gemma_io.h | 64 vector<int> &indicator_snp, const double &maf_level, 72 vector<int> &indicator_snp, vector<SNPINFO> &snpInfo, 91 vector<int> &indicator_snp, const int k_mode, 94 bool PlinkKin(const string &file_bed, vector<int> &indicator_snp, 98 vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K, 101 vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K, 104 vector<int> &indicator_snp, 109 vector<int> &indicator_snp, vector<vector<unsigned char>> &Xt, 135 const vector<int> &indicator_snp, 142 const vector<int> &indicator_snp,
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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, 114 vector<int> &indicator_idv, vector<int> &indicator_snp, 117 vector<int> &indicator_idv, vector<int> &indicator_snp,
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H A D | param.cpp | 288 ns_total = indicator_snp.size(); in ReadFiles() 324 ns_total = indicator_snp.size(); in ReadFiles() 378 ns_total += indicator_snp.size(); in ReadFiles() 1862 if (indicator_snp[i] == 0) { in WriteVar() 1871 if (indicator_snp[i] == 0) { in WriteVar() 2226 if (indicator_snp[i] == 0) { in ObtainWeight() 2254 if (indicator_snp[i] == 0) { in ObtainWeight() 2363 if (indicator_snp[i] == 0) { in UpdateSNPnZ() 2381 indicator_snp[i] = 0; in UpdateSNPnZ() 2422 if (indicator_snp[i] == 0) { in UpdateSNP() [all …]
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H A D | ldr.cpp | 65 indicator_snp = cPar.indicator_snp; in CopyFromParam()
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H A D | gemma_io.cpp | 644 indicator_snp.clear(); in ReadFile_geno() 709 indicator_snp.push_back(0); in ReadFile_geno() 795 indicator_snp.push_back(0); in ReadFile_geno() 801 indicator_snp.push_back(0); in ReadFile_geno() 807 indicator_snp.push_back(0); in ReadFile_geno() 840 indicator_snp.push_back(1); in ReadFile_geno() 866 indicator_snp.clear(); in ReadFile_bed() 1031 indicator_snp.push_back(1); in ReadFile_bed() 1437 if (indicator_snp[t] == 0) in BimbamKin() 1626 if (indicator_snp[t] == 0) { in PlinkKin() [all …]
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H A D | lm.cpp | 71 indicator_snp = cPar.indicator_snp; in CopyFromParam() 191 if (indicator_snp[i] == 0) { in WriteFiles() 421 for (size_t t = 0; t < indicator_snp.size(); ++t) { in AnalyzeBimbam() 426 if (indicator_snp[t] == 0) { in AnalyzeBimbam() 552 if (indicator_snp[t] == 0) { in AnalyzePlink()
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H A D | ldr.h | 54 vector<int> indicator_snp; variable
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H A D | varcov.h | 40 vector<int> indicator_snp; variable
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H A D | lm.h | 57 vector<int> indicator_snp; variable
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H A D | vc.cpp | 2244 for (size_t t = 0; t < indicator_snp.size(); ++t) { in BimbamXwz() 2247 ProgressBar("Reading SNPs ", t, indicator_snp.size() - 1); in BimbamXwz() 2249 if (indicator_snp[t] == 0) { in BimbamXwz() 2353 for (size_t t = 0; t < indicator_snp.size(); ++t) { in PlinkXwz() 2355 ProgressBar("Reading SNPs ", t, indicator_snp.size() - 1); in PlinkXwz() 2357 if (indicator_snp[t] == 0) { in PlinkXwz() 2497 for (size_t t = 0; t < indicator_snp.size(); ++t) { in BimbamXtXwz() 2500 ProgressBar("Reading SNPs ", t, indicator_snp.size() - 1); in BimbamXtXwz() 2502 if (indicator_snp[t] == 0) { in BimbamXtXwz() 2603 for (size_t t = 0; t < indicator_snp.size(); ++t) { in PlinkXtXwz() [all …]
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H A D | mvlmm.h | 71 vector<int> indicator_snp; variable
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H A D | bslmmdap.h | 72 vector<int> indicator_snp; variable
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H A D | lmm.h | 84 vector<int> indicator_snp; variable
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H A D | lmm.cpp | 82 indicator_snp = cPar.indicator_snp; in CopyFromParam() 200 if (indicator_snp[i] == 0) in WriteFiles() 1554 const auto num_snps = indicator_snp.size(); in Analyze() 1566 if (indicator_snp[t] == 0) in Analyze() 1751 if (indicator_snp[t] == 0) in AnalyzePlink() 1759 if (indicator_snp[t] == 0) { in AnalyzePlink() 2268 for (size_t t = 0; t < indicator_snp.size(); ++t) { in AnalyzeBimbamGXE() 2273 if (indicator_snp[t] == 0) { in AnalyzeBimbamGXE() 2433 if (indicator_snp[t] == 0) { in AnalyzePlinkGXE()
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H A D | bslmm.h | 86 vector<int> indicator_snp; variable
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H A D | bslmmdap.cpp | 87 indicator_snp = cPar.indicator_snp; in CopyFromParam() 387 if (indicator_snp[i] == 0) { in WriteResult()
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H A D | param.h | 287 vector<int> indicator_snp; variable
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H A D | bslmm.cpp | 98 indicator_snp = cPar.indicator_snp; in CopyFromParam() 170 if (indicator_snp[i] == 0) { in WriteParam() 220 if (indicator_snp[i] == 0) { in WriteParam()
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H A D | mvlmm.cpp | 87 indicator_snp = cPar.indicator_snp; in CopyFromParam() 169 if (indicator_snp[i] == 0) { in WriteFiles() 3203 for (size_t t = 0; t < indicator_snp.size(); ++t) { in AnalyzeBimbam() 3204 if (indicator_snp[t] == 0) { in AnalyzeBimbam() 3209 for (size_t t = 0; t < indicator_snp.size(); ++t) { in AnalyzeBimbam() 3214 if (indicator_snp[t] == 0) { in AnalyzeBimbam() 3662 for (size_t t = 0; t < indicator_snp.size(); ++t) { in AnalyzePlink() 3663 if (indicator_snp[t] == 0) { in AnalyzePlink() 3672 if (indicator_snp[t] == 0) { in AnalyzePlink() 4200 if (indicator_snp[t] == 0) { in AnalyzeBimbamGXE() [all …]
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H A D | gemma.cpp | 2480 PlinkXwz(file_str, cPar.d_pace, cPar.indicator_idv, cPar.indicator_snp, in BatchRun() 2484 cPar.indicator_snp, vec_cat, w1, z, 0, Xz); in BatchRun() 2501 PlinkXwz(file_str, cPar.d_pace, cPar.indicator_idv, cPar.indicator_snp, in BatchRun() 2505 cPar.indicator_snp, vec_cat, w, z, 0, XWz); in BatchRun() 2520 PlinkXtXwz(file_str, cPar.d_pace, cPar.indicator_idv, cPar.indicator_snp, in BatchRun() 2524 cPar.indicator_snp, XWz, 0, XtXWz); in BatchRun()
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