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authorZachary Sloan2013-04-16 22:15:47 +0000
committerZachary Sloan2013-04-16 22:15:47 +0000
commitaca3001513959116fdbe93eadaa4c2041a49d093 (patch)
treebbc028c3f76714fc8bfd8b58dcb96b3b37f5cf7f /wqflask
parent8fc2b9be64875bab87425d990874c849d9e1adf4 (diff)
downloadgenenetwork2-aca3001513959116fdbe93eadaa4c2041a49d093.tar.gz
Checking in before making some changes
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py41
1 files changed, 22 insertions, 19 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 3344b024..d9189f30 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -66,26 +66,29 @@ def run_human(pheno_vector,
with Bench("snp iterator loop"):
count = 0
for snp, this_id in plink_input:
- if count > 10000:
- break
- count += 1
-
- percent_complete = (float(count) / total_snps) * 100
- #print("percent_complete: ", percent_complete)
- temp_data.store("percent_complete", percent_complete)
+ with Bench("part before association"):
+ if count > 10000:
+ break
+ count += 1
+
+ percent_complete = (float(count) / total_snps) * 100
+ #print("percent_complete: ", percent_complete)
+ temp_data.store("percent_complete", percent_complete)
+
+ with Bench("actual association"):
+ ps, ts = human_association(snp,
+ n,
+ keep,
+ lmm_ob,
+ pheno_vector,
+ covariate_matrix,
+ kinship_matrix,
+ refit)
+
+ with Bench("after association"):
+ p_values.append(ps)
+ t_stats.append(ts)
- ps, ts = human_association(snp,
- n,
- keep,
- lmm_ob,
- pheno_vector,
- covariate_matrix,
- kinship_matrix,
- refit)
-
- p_values.append(ps)
- t_stats.append(ts)
-
return p_values, t_stats