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| author | Alexander Kabui | 2021-04-16 02:42:02 +0300 |
|---|---|---|
| committer | Alexander Kabui | 2021-04-16 02:42:02 +0300 |
| commit | 114f80d96d8bd8742b74a0aefdcbdcd22c42767b (patch) | |
| tree | ba5c66284cd7e484009b4b1c8a1533842140ca1c | |
| parent | 6c14eccb7a10cc598d4fa7ee4036cb44bddd9627 (diff) | |
| download | genenetwork3-114f80d96d8bd8742b74a0aefdcbdcd22c42767b.tar.gz | |
add benchmark function for sample r
| -rw-r--r-- | gn3/computations/correlations.py | 54 |
1 files changed, 27 insertions, 27 deletions
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py index 90b6c8c..a311b8d 100644 --- a/gn3/computations/correlations.py +++ b/gn3/computations/correlations.py @@ -152,42 +152,42 @@ def compute_all_sample_correlation(this_trait, return corr_results - def benchmark_compute_all_sample(this_trait, - target_datasets, - corr_method="pearson") ->List: - """Temp function to benchmark with compute_all_sample_r - """ +def benchmark_compute_all_sample(this_trait, + target_dataset, + corr_method="pearson") ->List: + """Temp function to benchmark with compute_all_sample_r + """ - this_trait_samples = this_trait["trait_sample_data"] + this_trait_samples = this_trait["trait_sample_data"] - corr_results = [] + corr_results = [] - for target_trait in target_dataset: - trait_id = target_trait.get("trait_id") - target_trait_data = target_trait["trait_sample_data"] - this_vals, target_vals = filter_shared_sample_keys( - this_trait_samples, target_trait_data) + for target_trait in target_dataset: + trait_id = target_trait.get("trait_id") + target_trait_data = target_trait["trait_sample_data"] + this_vals, target_vals = filter_shared_sample_keys( + this_trait_samples, target_trait_data) - sample_correlation = compute_sample_r_correlation( - corr_method=corr_method, - trait_vals=this_vals, - target_samples_vals=target_vals) + sample_correlation = compute_sample_r_correlation( + corr_method=corr_method, + trait_vals=this_vals, + target_samples_vals=target_vals) - if sample_correlation is not None: - (corr_coeffient, p_value, num_overlap) = sample_correlation + if sample_correlation is not None: + (corr_coeffient, p_value, num_overlap) = sample_correlation - else: - continue + else: + continue - corr_result = { - "corr_coeffient": corr_coeffient, - "p_value": p_value, - "num_overlap": num_overlap - } + corr_result = { + "corr_coeffient": corr_coeffient, + "p_value": p_value, + "num_overlap": num_overlap + } - corr_results.append({trait_id: corr_result}) + corr_results.append({trait_id: corr_result}) - return corr_results + return corr_results def tissue_lit_corr_for_probe_type(corr_type: str, top_corr_results): |