skip seak association testing if all burdens are constant (#142)

* skip seak association testing if all burdens are constant * fixup! Format Python code with psf/black pull_request --------- Co-authored-by: PMBio <[email protected]>
PMBio · Oct 28, 2024 · 113fa72 · 113fa72
1 parent 54e9057
commit 113fa72
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/deeprvat/deeprvat/associate.py b/deeprvat/deeprvat/associate.py
@@ -1152,6 +1152,9 @@ def regress_on_gene_scoretest(
         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}")