remove model frame, store terms and offsets instead

cole-trapnell-lab · May 22, 2024 · b11ca90 · b11ca90
1 parent c1871b1
commit b11ca90
Showing 1 changed file with 11 additions and 4 deletions.
diff --git a/R/cell_count_model.R b/R/cell_count_model.R
@@ -732,10 +732,14 @@ new_cell_count_model <- function(ccs,
   # model_frame = model.frame(full_model_formula[-2], pln_data)
   # xlevels = .getXlevels(terms(model_frame), model_frame)
   full_model_frame = model.frame(full_model_formula[-2], pln_data)
+  full_model_terms = terms(full_model_frame)
   full_model_xlevels = .getXlevels(terms(full_model_frame), full_model_frame)
+  full_model_offsets = model.offset(full_model_frame)
 
   reduced_model_frame = model.frame(reduced_model_formula[-2], pln_data)
+  reduced_model_terms = terms(reduced_model_frame)
   reduced_model_xlevels = .getXlevels(terms(reduced_model_frame), reduced_model_frame)
+  reduced_model_offsets = model.offset(reduced_model_frame)
 
   # Choose a model that isn't very aggressively sparsified
   best_reduced_model <- PLNmodels::getBestModel(reduced_pln_model, "EBIC")
@@ -778,11 +782,14 @@ new_cell_count_model <- function(ccs,
                       best_reduced_model = best_reduced_model,
                       reduced_model_family = reduced_pln_model,
                       sparsity = sparsity_factor,
-                      # model_aux = SimpleList(model_frame=model_frame, xlevels=xlevels),
-                      model_aux = SimpleList(full_model_frame=full_model_frame,
+                      model_aux = SimpleList(full_model_terms=full_model_terms, 
+                                             # full_model_frame=full_model_frame,
                                              full_model_xlevels=full_model_xlevels,
-                                             reduced_model_frame=reduced_model_frame,
-                                             reduced_model_xlevels=reduced_model_xlevels),
+                                             full_model_offsets=full_model_offsets,
+                                             reduced_model_terms=reduced_model_terms,
+                                             # reduced_model_frame=reduced_model_frame,
+                                             reduced_model_xlevels=reduced_model_xlevels, 
+                                             reduced_model_offsets=reduced_model_offsets ),
                       vhat = vhat,
                       vhat_method = vhat_method,
                       info=SimpleList()