From c49fd4d1bdbf4c7aed8b83e889e702f3965c8cb0 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 15 Dec 2020 12:46:29 +0000
Subject: Introduced `-lmm 9` switch for gemma to capture additive effect
 together without the log likelihood without adding computation time. See also
 #237

Closes #237
---
 src/lmm.cpp | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

(limited to 'src/lmm.cpp')

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);
       }
-- 
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