Merge pull request #47 from compneurobilbao/feature-selective-covar-c…

…orrection ENH: Feature selective covar correction
compneurobilbao · Sep 23, 2024 · 8a05ad5 · 8a05ad5
2 parents b8785e6 + 480bcbc
commit 8a05ad5
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Showing 4 changed files with 314 additions and 196 deletions.
diff --git a/src/ageml/commands.py b/src/ageml/commands.py
@@ -227,9 +227,13 @@ def configure_parser(self):
             help=messages.factors_long_description,
         )
 
-        # Optional arguments
-        self.parser.add_argument("--covariates", metavar="FILE", help=messages.covar_long_description)
-        self.parser.add_argument("--clinical", metavar="FILE", help=messages.clinical_long_description)
+        self.parser.add_argument("--covariates", metavar="FILE", required=False,
+                                 help=messages.covar_long_description)
+        self.parser.add_argument("--clinical", metavar="FILE", required=False,
+                                 help=messages.clinical_long_description)
+        self.parser.add_argument("--covcorr_mode", metavar="MODE", required=False,
+                                 choices=["cn", "each", "all"],
+                                 help=messages.covcorr_mode_long_description)
 
 
 class ClinicalGroups(Interface):
@@ -280,7 +284,11 @@ def configure_parser(self):
         )
 
         # Optional arguments
-        self.parser.add_argument("--covariates", metavar="FILE", help=messages.covar_long_description)
+        self.parser.add_argument("--covariates", metavar="FILE", required=False,
+                                 help=messages.covar_long_description)
+        self.parser.add_argument("--covcorr_mode", metavar="MODE", required=False,
+                                 choices=["cn", "each", "all"],
+                                 help=messages.covcorr_mode_long_description)
 
 
 class ClinicalClassification(Interface):
@@ -364,8 +372,12 @@ def configure_parser(self):
         )
 
         # Optional arguments
-        self.parser.add_argument("--covariates", metavar="FILE", help=messages.covar_long_description)
-
+        self.parser.add_argument("--covariates", metavar="FILE", required=False,
+                                 help=messages.covar_long_description)
+        self.parser.add_argument("--covcorr_mode", metavar="MODE", required=False,
+                                 choices=["cn", "each", "all"],
+                                 help=messages.covcorr_mode_long_description)
+
     def configure_args(self, args):
         """Configure argumens with required fromatting for modelling.
 

diff --git a/src/ageml/messages.py b/src/ageml/messages.py
@@ -73,6 +73,14 @@
     "https://github.com/compneurobilbao/ageml/blob/main/docs/input_file_specification.md#clinical-file"
 )
 
+covcorr_mode_long_description = (
+    "Mode for covariate correlation.\n"
+    "Must be one of 'cn', 'each', or 'all'. Default is 'cn'.\n"
+    "cn: Covariate correction is done using only the control group subjects.\n"
+    "all: Covariate correction is done using the whole dataset, all subjects.\n"
+    "each: Covariate correction is done for each clinical group subjects separately.\n"
+)
+
 systems_long_description = (
     "Path to input .txt file containing the features to use to model each system. \n"
     "Each new line corresponds to a different system. The parser follows a formatting \n"