aboutsummaryrefslogtreecommitdiff
path: root/gn3/computations
diff options
context:
space:
mode:
authorAlexander Kabui2021-10-29 09:49:28 +0300
committerGitHub2021-10-29 09:49:28 +0300
commit8f036415975d6e224e5e94277997329c0f1fa159 (patch)
treeabc1e4b8578fad0cc934b334edc5c573a4bd6d20 /gn3/computations
parent0cfff99e22155b6b15e23cbeff596f5f8f08709c (diff)
downloadgenenetwork3-8f036415975d6e224e5e94277997329c0f1fa159.tar.gz
Feature/biweight reimplementation (#47)
* add biweight reimplementation with pingouin * delete biweight scripts and tests * add python-pingouin to guix file * delete biweight paths * mypy fix:pingouin mising imports * pep8 formatting && pylint fixes
Diffstat (limited to 'gn3/computations')
-rw-r--r--gn3/computations/biweight.py27
-rw-r--r--gn3/computations/correlations.py11
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,