diff options
Diffstat (limited to 'src/lm.cpp')
| -rw-r--r-- | src/lm.cpp | 24 |
1 files changed, 12 insertions, 12 deletions
diff --git a/src/lm.cpp b/src/lm.cpp index b4bc010..f8cb974 100644 --- a/src/lm.cpp +++ b/src/lm.cpp @@ -41,6 +41,7 @@ #include "gsl/gsl_min.h" #include "gsl/gsl_integration.h" +#include "eigenlib.h" #include "gzstream.h" #include "lapack.h" @@ -519,9 +520,9 @@ void LM::Analyzebgen (const gsl_matrix *W, const gsl_vector *y) for (size_t i=0; i<ni_test; ++i) { if (gsl_vector_get (x_miss, i)==0) {gsl_vector_set(x, i, x_mean);} geno=gsl_vector_get(x, i); - if (x_mean>1) { - gsl_vector_set(x, i, 2-geno); - } + //if (x_mean>1) { + //gsl_vector_set(x, i, 2-geno); + //} } @@ -626,9 +627,9 @@ void LM::AnalyzeBimbam (const gsl_matrix *W, const gsl_vector *y) for (size_t i=0; i<ni_test; ++i) { if (gsl_vector_get (x_miss, i)==0) {gsl_vector_set(x, i, x_mean);} geno=gsl_vector_get(x, i); - if (x_mean>1) { - gsl_vector_set(x, i, 2-geno); - } + //if (x_mean>1) { + //gsl_vector_set(x, i, 2-geno); + //} } //calculate statistics @@ -712,7 +713,6 @@ void LM::AnalyzePlink (const gsl_matrix *W, const gsl_vector *y) b=ch[0]; } - for (vector<SNPINFO>::size_type t=0; t<snpInfo.size(); ++t) { if (t%d_pace==0 || t==snpInfo.size()-1) {ProgressBar ("Reading SNPs ", t, snpInfo.size()-1);} if (indicator_snp[t]==0) {continue;} @@ -747,9 +747,9 @@ void LM::AnalyzePlink (const gsl_matrix *W, const gsl_vector *y) for (size_t i=0; i<ni_test; ++i) { geno=gsl_vector_get(x,i); if (geno==-9) {gsl_vector_set(x, i, x_mean); geno=x_mean;} - if (x_mean>1) { - gsl_vector_set(x, i, 2-geno); - } + //if (x_mean>1) { + //gsl_vector_set(x, i, 2-geno); + //} } //calculate statistics @@ -759,11 +759,11 @@ void LM::AnalyzePlink (const gsl_matrix *W, const gsl_vector *y) CalcvPv(WtWi, Wty, Wtx, y, x, xPwy, xPwx); LmCalcP (a_mode-50, yPwy, xPwy, xPwx, df, W->size1, beta, se, p_wald, p_lrt, p_score); - time_opt+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); - //store summary data SUMSTAT SNPs={beta, se, 0.0, 0.0, p_wald, p_lrt, p_score}; sumStat.push_back(SNPs); + + time_opt+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0); } cout<<endl; |