aboutsummaryrefslogtreecommitdiff
path: root/gn3
diff options
context:
space:
mode:
authorFrederick Muriuki Muriithi2021-11-01 08:33:26 +0300
committerFrederick Muriuki Muriithi2021-11-01 08:33:26 +0300
commitb56341f9144623cc41bc815b337490ace04b2495 (patch)
treee568d94460585155d752bdf75fd7205699251bf2 /gn3
parent37cf87e94a44ba2ab26a8e458e0c5a90fe5ecc7a (diff)
parent8f036415975d6e224e5e94277997329c0f1fa159 (diff)
downloadgenenetwork3-b56341f9144623cc41bc815b337490ace04b2495.tar.gz
Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-correlations
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/biweight.py27
-rw-r--r--gn3/computations/correlations.py11
-rw-r--r--gn3/settings.py3
3 files changed, 5 insertions, 36 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,
diff --git a/gn3/settings.py b/gn3/settings.py
index d5f1d3c..e85eeff 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -22,9 +22,6 @@ SQLALCHEMY_TRACK_MODIFICATIONS = False
GN2_BASE_URL = "http://www.genenetwork.org/"
-# biweight script
-BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R"
-
# wgcna script
WGCNA_RSCRIPT = "wgcna_analysis.R"
# qtlreaper command