| /dports/biology/gemma/GEMMA-0.98.3/src/ |
| H A D | vc.h | 85 const gsl_matrix *Svar_mat);
93 const gsl_matrix *Svar_mat, const gsl_vector *q_vec,
126 const gsl_matrix *Svar_mat, const gsl_vector *w,
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| H A D | gemma_io.h | 176 gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);
180 gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);
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| H A D | vc.cpp | 116 const gsl_matrix *Svar_mat) { in WriteFile_qs() argument
155 for (size_t i = 0; i < Svar_mat->size1; i++) { in WriteFile_qs()
156 for (size_t j = 0; j < Svar_mat->size2; j++) { in WriteFile_qs()
157 outfile_s << gsl_matrix_get(Svar_mat, i, j) << "\t"; in WriteFile_qs()
1010 gsl_matrix *Svar_mat, gsl_vector *qvar_vec, size_t &ni_total, in ReadFile_cor() argument
1288 gsl_matrix_set(Svar_mat, i, j, 2.0 * mat_Svar[i][i] * ns_test * in ReadFile_cor()
1292 gsl_matrix_set(Svar_mat, i, j, 2.0 * (mat_Svar[i][j] + mat_Svar[j][i]) * in ReadFile_cor()
1310 const gsl_matrix *Svar_mat, const gsl_vector *q_vec, in CalcVCss() argument
1354 d = gsl_matrix_get(Svar_mat, i, j); in CalcVCss()
2729 const gsl_matrix *Svar_mat, const gsl_vector *w, in CalcCIss() argument
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| H A D | gemma.cpp | 1952 gsl_matrix_view Svar_mat = in BatchRun() local
1972 cPar.CalcS(mapRS2wA, mapRS2wK, W, A, K, &S_mat.matrix, &Svar_mat.matrix, in BatchRun()
2137 gsl_matrix_view Svar_mat = in BatchRun() local
2161 cPar.CalcS(mapRS2wA, mapRS2wK, W, A, K, &S_mat.matrix, &Svar_mat.matrix, in BatchRun()
2170 CalcVCss(Vq, &S_mat.matrix, &Svar_mat.matrix, q, &s_vec.vector, in BatchRun()
2193 cPar.CalcS(mapRS2wA, mapRS2wK, W, A, K, &S_mat.matrix, &Svar_mat.matrix, in BatchRun()
2202 CalcVCss(Vq, &S_mat.matrix, &Svar_mat.matrix, q, &s_vec.vector, in BatchRun()
2264 gsl_matrix_view Svar_mat = in BatchRun() local
2281 ReadFile_ref(cPar.file_ref, &S_mat.matrix, &Svar_mat.matrix, s_ref, in BatchRun()
2284 ReadFile_mref(cPar.file_mref, &S_mat.matrix, &Svar_mat.matrix, s_ref, in BatchRun()
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| H A D | gemma_io.cpp | 3972 gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni) { in ReadFile_ref() argument
3980 ReadFile_matrix(Sfile, S_mat, Svar_mat); in ReadFile_ref()
4087 gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni) { in ReadFile_mref() argument
4090 gsl_matrix_set_zero(Svar_mat); in ReadFile_mref()
4095 gsl_matrix *Svar_sub = gsl_matrix_safe_alloc(Svar_mat->size1, Svar_mat->size2); in ReadFile_mref()
4135 gsl_matrix_add(Svar_mat, Svar_sub); in ReadFile_mref()
4156 d = gsl_matrix_get(Svar_mat, i, j) / (d1 * d2 * d1 * d2); in ReadFile_mref()
4157 gsl_matrix_set(Svar_mat, i, j, d); in ReadFile_mref()
4159 gsl_matrix_set(Svar_mat, j, i, d); in ReadFile_mref()
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