From 89a7868175c7594be91d638974ac1054fc3c8659 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 31 May 2022 17:55:58 +0000
Subject: Reverse polarity for gemma additive effects

This is basically just a quick pseudo-fix to at least get the polarity
right
---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 623ab87f..ec12f9b7 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -220,7 +220,7 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
                         marker['chr'] = line.split("\t")[0]
                     marker['Mb'] = float(line.split("\t")[2]) / 1000000
                     marker['p_value'] = float(line.split("\t")[10])
-                    marker['additive'] = float(line.split("\t")[7])
+                    marker['additive'] = -(float(line.split("\t")[7]))
                     if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                         marker['lod_score'] = 0
                     else:
-- 
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