From 3fd01d2e09515e7b392954baa0ab92c98b6d7f00 Mon Sep 17 00:00:00 2001
From: Brian Clarke <9725212+bfclarke@users.noreply.github.com>
Date: Fri, 8 Nov 2024 15:56:42 +0100
Subject: [PATCH] adjust offset/scaling

---
 deeprvat/deeprvat/associate.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/deeprvat/deeprvat/associate.py b/deeprvat/deeprvat/associate.py
index 2fd117bf..684f59e3 100644
--- 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(