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Searched refs:indicator_snp (Results 1 – 21 of 21) sorted by relevance

/dports/biology/gemma/GEMMA-0.98.3/src/
H A Dvarcov.cpp63 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()
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H A Dgemma_io.h64 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,
H A Dvc.h100 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,
H A Dparam.cpp288 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()
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H A Dldr.cpp65 indicator_snp = cPar.indicator_snp; in CopyFromParam()
H A Dgemma_io.cpp644 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()
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H A Dlm.cpp71 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()
H A Dldr.h54 vector<int> indicator_snp; variable
H A Dvarcov.h40 vector<int> indicator_snp; variable
H A Dlm.h57 vector<int> indicator_snp; variable
H A Dvc.cpp2244 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 …]
H A Dmvlmm.h71 vector<int> indicator_snp; variable
H A Dbslmmdap.h72 vector<int> indicator_snp; variable
H A Dlmm.h84 vector<int> indicator_snp; variable
H A Dlmm.cpp82 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()
H A Dbslmm.h86 vector<int> indicator_snp; variable
H A Dbslmmdap.cpp87 indicator_snp = cPar.indicator_snp; in CopyFromParam()
387 if (indicator_snp[i] == 0) { in WriteResult()
H A Dparam.h287 vector<int> indicator_snp; variable
H A Dbslmm.cpp98 indicator_snp = cPar.indicator_snp; in CopyFromParam()
170 if (indicator_snp[i] == 0) { in WriteParam()
220 if (indicator_snp[i] == 0) { in WriteParam()
H A Dmvlmm.cpp87 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()
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H A Dgemma.cpp2480 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()