From 63a6ab2f565611bbe1464d718acff4398de12a19 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 15 Aug 2013 17:08:20 -0500
Subject: Removed the markers with no variance (and thus no p-values) from the
 manhattan plot

---
 wqflask/base/data_set.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 091433a6..0b9b1ce0 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -168,11 +168,13 @@ class Markers(object):
         
         for marker, p_value in itertools.izip(self.markers, p_values):
             marker['p_value'] = p_value
-            if math.isnan(marker['p_value']):
-                print("p_value is:", marker['p_value'])
-            marker['lod_score'] = -math.log10(marker['p_value'])
-            #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
-            marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
+            if marker['p_value'] == 0:
+                marker['lod_score'] = 0
+                marker['lrs_value'] = 0
+            else:
+                marker['lod_score'] = -math.log10(marker['p_value'])
+                #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
+                marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
         
         
 
-- 
cgit v1.2.3