diff options
| -rw-r--r-- | gn3/computations/correlations2.py | 21 | ||||
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 5 |
2 files changed, 7 insertions, 19 deletions
diff --git a/gn3/computations/correlations2.py b/gn3/computations/correlations2.py index 69921b1..d0222ae 100644 --- a/gn3/computations/correlations2.py +++ b/gn3/computations/correlations2.py @@ -6,7 +6,7 @@ FUNCTIONS: compute_correlation: TODO: Describe what the function does...""" -from math import sqrt +from scipy import stats ## From GN1: mostly for clustering and heatmap generation def __items_with_values(dbdata, userdata): @@ -16,24 +16,11 @@ def __items_with_values(dbdata, userdata): return tuple(zip(*filtered)) if filtered else ([], []) def compute_correlation(dbdata, userdata): - """Compute some form of correlation. + """Compute the Pearson correlation coefficient. This is extracted from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/webqtlUtil.py#L622-L647 """ x_items, y_items = __items_with_values(dbdata, userdata) - if len(x_items) < 6: - return (0.0, len(x_items)) - meanx = sum(x_items)/len(x_items) - meany = sum(y_items)/len(y_items) - def cal_corr_vals(acc, item): - xitem, yitem = item - return [ - acc[0] + ((xitem - meanx) * (yitem - meany)), - acc[1] + ((xitem - meanx) * (xitem - meanx)), - acc[2] + ((yitem - meany) * (yitem - meany))] - xyd, sxd, syd = reduce(cal_corr_vals, zip(x_items, y_items), [0.0, 0.0, 0.0]) - try: - return ((xyd/(sqrt(sxd)*sqrt(syd))), len(x_items)) - except ZeroDivisionError: - return(0, len(x_items)) + correlation = stats.pearsonr(x_items, y_items)[0] if len(x_items) >= 6 else 0 + return (correlation, len(x_items)) diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py index e6cf198..d60dd62 100644 --- a/tests/unit/computations/test_correlation.py +++ b/tests/unit/computations/test_correlation.py @@ -4,6 +4,7 @@ from unittest import mock import unittest from collections import namedtuple +import math from numpy.testing import assert_almost_equal from gn3.computations.correlations import normalize_values @@ -471,10 +472,10 @@ class TestCorrelation(TestCase): [None, None, None, None, None, None, None, None, None, 0], (0.0, 1)], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], - (0, 10)], + (math.nan, 10)], [[9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87], [9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87], - (0.9999999999999998, 10)], + (math.nan, 10)], [[9.3, 2.2, 5.4, 7.2, 6.4, 7.6, 3.8, 1.8, 8.4, 0.2], [0.6, 3.97, 5.82, 8.21, 1.65, 4.55, 6.72, 9.5, 7.33, 2.34], (-0.12720361919462056, 10)], |