diff options
| -rw-r--r-- | src/lmm.cpp | 13 | ||||
| -rw-r--r-- | src/param.cpp | 1 |
2 files changed, 9 insertions, 5 deletions
diff --git a/src/lmm.cpp b/src/lmm.cpp index 54ab08e..aef9a0c 100644 --- a/src/lmm.cpp +++ b/src/lmm.cpp @@ -115,7 +115,7 @@ void LMM::WriteFiles() { outfile << "se" << "\t"; } - if (a_mode != M_LMM3) + if (a_mode != M_LMM3 && a_mode != M_LMM9) outfile << "logl_H1" << "\t"; switch(a_mode) { @@ -124,6 +124,7 @@ void LMM::WriteFiles() { << "p_wald" << endl; break; case M_LMM2: + case M_LMM9: outfile << "l_mle" << "\t" << "p_lrt" << endl; break; @@ -148,7 +149,7 @@ void LMM::WriteFiles() { outfile << st.se << "\t"; } - if (a_mode != M_LMM3) + if (a_mode != M_LMM3 && a_mode != M_LMM9) outfile << st.logl_H1 << "\t"; switch(a_mode) { @@ -157,6 +158,7 @@ void LMM::WriteFiles() { << st.p_wald << endl; break; case M_LMM2: + case M_LMM9: outfile << st.lambda_mle << "\t" << st.p_lrt << endl; break; @@ -174,6 +176,7 @@ void LMM::WriteFiles() { }; + if (!file_gene.empty()) { outfile << "geneID" << "\t"; @@ -1527,17 +1530,17 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp, double logl_H1 = 0.0; // 3 is before 1. - if (a_mode == 3 || a_mode == 4) { + if (a_mode == M_LMM3 || a_mode == M_LMM4 || a_mode == M_LMM9 ) { CalcRLScore(l_mle_null, param1, beta, se, p_score); } - if (a_mode == 1 || a_mode == 4) { + if (a_mode == M_LMM1 || a_mode == M_LMM4) { // for univariate a_mode is 1 CalcLambda('R', param1, l_min, l_max, n_region, lambda_remle, logl_H1); CalcRLWald(lambda_remle, param1, beta, se, p_wald); } - if (a_mode == 2 || a_mode == 4) { + if (a_mode == M_LMM2 || a_mode == M_LMM9 || a_mode == M_LMM4) { CalcLambda('L', param1, l_min, l_max, n_region, lambda_mle, logl_H1); p_lrt = gsl_cdf_chisq_Q(2.0 * (logl_H1 - logl_mle_H0), 1); } diff --git a/src/param.cpp b/src/param.cpp index db6d8d5..5f2871e 100644 --- a/src/param.cpp +++ b/src/param.cpp @@ -510,6 +510,7 @@ void PARAM::CheckParam(void) { error = true; } if (a_mode != 1 && a_mode != 2 && a_mode != 3 && a_mode != 4 && a_mode != 5 && + a_mode != M_LMM9 && a_mode != 11 && a_mode != 12 && a_mode != 13 && a_mode != 14 && a_mode != 15 && a_mode != 21 && a_mode != 22 && a_mode != 25 && a_mode != 26 && a_mode != 27 && a_mode != 28 && a_mode != 31 && |