Merge pull request #115 from zhaotianjing/master

fix a bug in nn-mm with no omics data
reworkhow · Mar 17, 2022 · a7d6be8 · a7d6be8
2 parents 3b3908a + 394ad8d
commit a7d6be8
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/src/1.JWAS/src/JWAS.jl b/src/1.JWAS/src/JWAS.jl
@@ -157,7 +157,7 @@ function runMCMC(mme::MME,df;
                 fitting_J_vector                = true,  #parameters for single-step analysis
                 causal_structure                = false,
                 mega_trait                      = mme.nonlinear_function == false ? false : true, #NNBayes -> default mega_trait=true
-                missing_phenotypes              = true,
+                missing_phenotypes              = mme.nonlinear_function == false ? true : false, #NN-MM -> missing hidden nodes will be sampled
                 constraint                      = false,
                 #Genomic Prediction
                 outputEBV                       = true,

diff --git a/src/1.JWAS/src/Nonlinear/nnbayes_check.jl b/src/1.JWAS/src/Nonlinear/nnbayes_check.jl
@@ -194,16 +194,15 @@ function nnlmm_initialize_missing(mme,df)
           end
         end
       end
-      # add indicators for individuals with full omics data, so their omics won't be sampled
-      n_observed_omics = sum(mme.missingPattern,dims=2) #number of observed omics for each ind
-      n_omics          = length(mme.lhsVec)             #number of omics
-      full_omics       = n_observed_omics .== n_omics   #indicator for ind with full omics
-      mme.incomplete_omics    = vec(.!full_omics)              #indicator for ind with no/partial omics
-
     else  #NN-Bayes with hidden nodes (G3 paper)
       #all omics should be missing, the missingPattern should be all 0
       #but we already set y1,...,y5 as yobs, so we have to build missingPattern
       # byhand.
       mme.missingPattern = .!ismissing.(Array{Missing}(missing, size(df[!,mme.lhsVec])))
     end
+    # add indicators for individuals with full omics data, so their omics won't be sampled
+    n_observed_omics = sum(mme.missingPattern,dims=2) #number of observed omics for each ind
+    n_omics          = length(mme.lhsVec)             #number of omics
+    full_omics       = n_observed_omics .== n_omics   #indicator for ind with full omics
+    mme.incomplete_omics    = vec(.!full_omics)              #indicator for ind with no/partial omics
 end