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| author | Frederick Muriuki Muriithi | 2021-11-01 08:33:26 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2021-11-01 08:33:26 +0300 |
| commit | b56341f9144623cc41bc815b337490ace04b2495 (patch) | |
| tree | e568d94460585155d752bdf75fd7205699251bf2 /gn3/computations | |
| parent | 37cf87e94a44ba2ab26a8e458e0c5a90fe5ecc7a (diff) | |
| parent | 8f036415975d6e224e5e94277997329c0f1fa159 (diff) | |
| download | genenetwork3-b56341f9144623cc41bc815b337490ace04b2495.tar.gz | |
Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-correlations
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/biweight.py | 27 | ||||
| -rw-r--r-- | gn3/computations/correlations.py | 11 |
2 files changed, 5 insertions, 33 deletions
diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py deleted file mode 100644 index 7accd0c..0000000 --- a/gn3/computations/biweight.py +++ /dev/null @@ -1,27 +0,0 @@ -"""module contains script to call biweight midcorrelation in R""" -import subprocess - -from typing import List -from typing import Tuple - -from gn3.settings import BIWEIGHT_RSCRIPT - - -def calculate_biweight_corr(trait_vals: List, - target_vals: List, - path_to_script: str = BIWEIGHT_RSCRIPT, - command: str = "Rscript" - ) -> Tuple[float, float]: - """biweight function""" - - args_1 = ' '.join(str(trait_val) for trait_val in trait_vals) - args_2 = ' '.join(str(target_val) for target_val in target_vals) - cmd = [command, path_to_script] + [args_1] + [args_2] - - results = subprocess.check_output(cmd, universal_newlines=True) - try: - (corr_coeff, p_val) = tuple( - [float(y.strip()) for y in results.split()]) - return (corr_coeff, p_val) - except Exception as error: - raise error diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py index bb13ff1..c930df0 100644 --- a/gn3/computations/correlations.py +++ b/gn3/computations/correlations.py @@ -8,7 +8,7 @@ from typing import Optional from typing import Callable import scipy.stats -from gn3.computations.biweight import calculate_biweight_corr +import pingouin as pg def map_shared_keys_to_values(target_sample_keys: List, @@ -102,11 +102,10 @@ package :not packaged in guix """ - try: - results = calculate_biweight_corr(x_val, y_val) - return results - except Exception as error: - raise error + results = pg.corr(x_val, y_val, method="bicor") + corr_coeff = results["r"].values[0] + p_val = results["p-val"].values[0] + return (corr_coeff, p_val) def filter_shared_sample_keys(this_samplelist, |