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authorMuriithi Frederick Muriuki2021-08-20 14:24:35 +0300
committerMuriithi Frederick Muriuki2021-08-20 14:24:35 +0300
commit0023b7a0e4a794444364b403cba72e07213c8419 (patch)
treec6613c66cb9d041acbea7f132c89a26203c2a1e0 /gn3/computations
parent96af4e9e32ed167a8d70cf7761b709b1a37bb344 (diff)
parentc9ee473ff7797f6bbd7507eb55c772a3a646acee (diff)
downloadgenenetwork3-0023b7a0e4a794444364b403cba72e07213c8419.tar.gz
Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_generation
Diffstat (limited to 'gn3/computations')
-rw-r--r--gn3/computations/correlations.py15
1 files changed, 7 insertions, 8 deletions
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index 8d76c09..bb13ff1 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -124,9 +124,9 @@ def filter_shared_sample_keys(this_samplelist,
return (this_vals, target_vals)
-def speed_compute_all_sample_correlation(this_trait,
- target_dataset,
- corr_method="pearson") -> List:
+def fast_compute_all_sample_correlation(this_trait,
+ target_dataset,
+ corr_method="pearson") -> List:
"""Given a trait data sample-list and target__datasets compute all sample
correlation
this functions uses multiprocessing if not use the normal fun
@@ -362,8 +362,7 @@ def compute_tissue_correlation(primary_tissue_dict: dict,
target_tissues_values=target_tissue_vals,
trait_id=trait_id,
corr_method=corr_method)
- tissue_result_dict = {trait_id: tissue_result}
- tissues_results.append(tissue_result_dict)
+ tissues_results.append(tissue_result)
return sorted(
tissues_results,
key=lambda trait_name: -abs(list(trait_name.values())[0]["tissue_corr"]))
@@ -386,9 +385,9 @@ def process_trait_symbol_dict(trait_symbol_dict, symbol_tissue_vals_dict) -> Lis
return traits_tissue_vals
-def speed_compute_tissue_correlation(primary_tissue_dict: dict,
- target_tissues_data: dict,
- corr_method: str):
+def fast_compute_tissue_correlation(primary_tissue_dict: dict,
+ target_tissues_data: dict,
+ corr_method: str):
"""Experimental function that uses multiprocessing for computing tissue
correlation