skip seak association testing if all burdens are constant

PMBio · Oct 21, 2024 · b9801d7 · b9801d7
1 parent 87d5f41
commit b9801d7
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/deeprvat/deeprvat/associate.py b/deeprvat/deeprvat/associate.py
@@ -1151,7 +1151,10 @@ def regress_on_gene_scoretest(
     if np.all(np.abs(burdens) < 1e-6):
         logger.warning(f"Burden for gene {gene} is 0 for all samples; skipping")
         return None
-
+
+    if np.unique(burdens).shape[0] == 1:
+        logger.warning(f"Burdens for gene {gene} are all constant; skipping")
+        return None
     pv = model_score.pv_alt_model(burdens)
 
     logger.info(f"p-value: {pv}")