add is_control to common dataset and clean up

openproblems-bio · Feb 4, 2025 · 0e4c0e1 · 0e4c0e1
1 parent 7136d76
commit 0e4c0e1
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/src/api/file_common_dataset.yaml b/src/api/file_common_dataset.yaml
@@ -31,6 +31,16 @@ info:
         name: group
         description: Biological group of the donor
         required: true
+      - type: integer
+        name: is_control
+        description: |
+          Whether the sample the cell came from can be used as a control for batch 
+          effect correction.
+          0: cannot be used as a control.
+          >= 1: can be used as a control.
+          For cells with >= 1: cells with the same value come from the same donor.
+          Different values indicate different donors.
+        required: true
     var:
       - type: integer
         name: numeric_id
@@ -52,11 +62,6 @@ info:
         name: to_correct
         description: Whether the marker will be batch corrected
         required: true
-    # obsm:
-    #   - type: double
-    #     name: X_pca
-    #     description: The resulting PCA embedding.
-    #     required: true
     uns:
       - type: string
         name: dataset_id

diff --git a/src/api/file_unintegrated_censored.yaml b/src/api/file_unintegrated_censored.yaml
@@ -57,11 +57,6 @@ info:
         name: to_correct
         description: Whether the marker will be batch corrected
         required: true
-    # obsm:
-    #   - type: double
-    #     name: X_pca
-    #     description: The resulting PCA embedding.
-    #     required: true
     uns:
       - type: string
         name: dataset_id