get_dataset_differential_expression_analyses has keep_non_specific ar…

…gument
PavlidisLab · Jul 10, 2024 · f379415 · f379415
1 parent 9ad44e2
commit f379415
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/gemmapy/gemmapy_api.py b/gemmapy/gemmapy_api.py
@@ -1563,7 +1563,8 @@ def make_anndata(pack):
         return out
 
     def get_differential_expression_values(self, 
-                                           dataset:Optional[str|int] = None, 
+                                           dataset:Optional[str|int] = None,
+                                           keep_non_specific:bool = False,
                                            result_sets:Optional[List[str|int]] = None,
                                            readable_contrasts:bool = False, 
                                            **kwargs)->List[DataFrame]:
@@ -1636,6 +1637,10 @@ def get_differential_expression_values(self,
 
         for rs in result_sets:
             df = self.__get_result_set(rs)
+
+            if not keep_non_specific:
+                df = df[~df.GeneSymbol.str.contains("|",regex = False,na = True)]
+
             if readable_contrasts:
                 factors = pd.concat(
                     list(all_factors[all_factors.result_ID == rs].experimental_factors)