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authorZachary Sloan2013-08-15 17:08:20 -0500
committerZachary Sloan2013-08-15 17:08:20 -0500
commit63a6ab2f565611bbe1464d718acff4398de12a19 (patch)
treefc40ab97c0bc975c65601e7ae3f0a78370db2c91 /wqflask/base/data_set.py
parent535208e73e8c1706734c0d466a535f01991d1b4f (diff)
downloadgenenetwork2-63a6ab2f565611bbe1464d718acff4398de12a19.tar.gz
Removed the markers with no variance (and thus no p-values) from the
manhattan plot
Diffstat (limited to 'wqflask/base/data_set.py')
-rwxr-xr-xwqflask/base/data_set.py12
1 files changed, 7 insertions, 5 deletions
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