adjust offset/scaling

PMBio · Nov 8, 2024 · 3fd01d2 · 3fd01d2
1 parent cbf432d
commit 3fd01d2
Showing 1 changed file with 6 additions and 3 deletions.
diff --git a/deeprvat/deeprvat/associate.py b/deeprvat/deeprvat/associate.py
@@ -464,9 +464,12 @@ def make_regenie_input_(
                     continue
 
                 # Rescale scores to fill out range [0, 1] (making dosages in [0, 2])
-                min_burden = np.min(this_burdens)
-                max_burden = np.max(this_burdens)
-                this_burdens = (this_burdens - min_burden) / (max_burden - min_burden)
+                # TODO:
+                # 1. Warn if burdens are censored to remain > 0
+                # 2. Offset/scale more intelligently to fill out [0, 1] better
+                # 3. (maybe) Allow for setting offset/scale as parameter
+                offset = 0.251
+                this_burdens = np.max(this_burdens - offset, 0)
 
                 # REGENIE assumes by default genotypes are stored alt-first
                 genotypes = np.stack(