diff options
Diffstat (limited to 'src/lmm.cpp')
| -rw-r--r-- | src/lmm.cpp | 15 |
1 files changed, 7 insertions, 8 deletions
diff --git a/src/lmm.cpp b/src/lmm.cpp index 08b4d41..10e3e53 100644 --- a/src/lmm.cpp +++ b/src/lmm.cpp @@ -153,7 +153,7 @@ void LMM::WriteFiles() { outfile << scientific << setprecision(6); if (a_mode != M_LMM2) { - outfile << st.beta << "\t"; + outfile << scientific << st.beta << "\t"; outfile << st.se << "\t"; } @@ -2103,14 +2103,13 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp, auto m = st.markerinfo; auto name = m.name; auto chr = m.chr; - auto pos = m.pos; outfile << chr << "\t"; outfile << name << "\t"; - outfile << pos << "\t"; - auto n_miss = 0; - outfile << n_miss << "\t-\t-\t"; // n_miss column - // outfile << st.maf << "\t" ; + outfile << m.pos << "\t"; + outfile << m.n_miss << "\t-\t-\t"; // n_miss column + allele1 + allele0 + outfile << fixed << setprecision(3) << m.maf << "\t"; + outfile << scientific << setprecision(6); if (a_mode != M_LMM2) { outfile << st.beta << "\t"; outfile << st.se << "\t"; @@ -2253,9 +2252,9 @@ void LMM::mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval, // compute maf and n_miss (NAs) size_t n_miss = 0; // count NAs: FIXME - double maf = compute_maf(ni_total, ni_test, n_miss, gs.data()); + double maf = compute_maf(ni_total, ni_test, n_miss, gs.data(), indicator_idv); - markerinfo = MarkerInfo { .name=marker,.chr=chr,.pos=pos,.line_no=num }; + markerinfo = MarkerInfo { .name=marker,.chr=chr,.pos=pos,.line_no=num,.n_miss=n_miss,.maf=maf }; // cout << "!!!!" << size << marker << ": af" << maf << " " << gs[0] << "," << gs[1] << "," << gs[2] << "," << gs[3] << endl; } |