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| author | Zachary Sloan | 2013-08-15 17:08:20 -0500 |
|---|---|---|
| committer | Zachary Sloan | 2013-08-15 17:08:20 -0500 |
| commit | 63a6ab2f565611bbe1464d718acff4398de12a19 (patch) | |
| tree | fc40ab97c0bc975c65601e7ae3f0a78370db2c91 /wqflask/wqflask | |
| parent | 535208e73e8c1706734c0d466a535f01991d1b4f (diff) | |
| download | genenetwork2-63a6ab2f565611bbe1464d718acff4398de12a19.tar.gz | |
Removed the markers with no variance (and thus no p-values) from the
manhattan plot
Diffstat (limited to 'wqflask/wqflask')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 4 |
1 files changed, 2 insertions, 2 deletions
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 |