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-rwxr-xr-xwqflask/base/data_set.py12
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py4
2 files changed, 9 insertions, 7 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
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 3743e77c..6ef1669b 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -396,7 +396,7 @@ def GWAS(pheno_vector,
keep = True - v
xs = x[keep,:]
if xs.var() == 0:
- p_values.append(np.nan)
+ p_values.append(0)
t_statistics.append(np.nan)
continue
@@ -413,7 +413,7 @@ def GWAS(pheno_vector,
ts, ps, beta, betaVar = lmm_ob_2.association(xs, REML=restricted_max_likelihood)
else:
if x.var() == 0:
- p_values.append(np.nan)
+ p_values.append(0)
t_statistics.append(np.nan)
continue