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authorFrederick Muriuki Muriithi2021-11-09 10:16:50 +0300
committerFrederick Muriuki Muriithi2021-11-09 10:16:50 +0300
commit89691df0d7ba096fb7a154aca3adf40f8dfaa8ae (patch)
tree8a6541abc927d554b6b57c1634763687d136db42 /gn3/computations
parentb38be1a60ea04e3087d36ff68e7b047922295d4e (diff)
downloadgenenetwork3-89691df0d7ba096fb7a154aca3adf40f8dfaa8ae.tar.gz
Implement remaining part of `partial_correlation_recursive` function
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: implement remaining portion of `partial_correlation_recursive` function. * tests/unit/computations/test_partial_correlations.py: add parsing for new data format and update tests
Diffstat (limited to 'gn3/computations')
-rw-r--r--gn3/computations/partial_correlations.py27
1 files changed, 26 insertions, 1 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 9d73197..07a67be 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -332,4 +332,29 @@ def partial_correlation_recursive(
(corrs["rxy"] - corrs["rxz"] * corrs["ryz"]) /
(math.sqrt(1 - corrs["rxz"]**2) *
math.sqrt(1 - corrs["ryz"]**2))), ROUND_TO)
- return round(0, ROUND_TO)
+
+ remaining_cols = [
+ colname for colname, series in data.items()
+ if colname not in ("x", "y", "z0")
+ ]
+
+ new_xdata = tuple(data["x"])
+ new_ydata = tuple(data["y"])
+ zc = tuple(
+ tuple(row_series[1])
+ for row_series in data[remaining_cols].iterrows())
+
+ rxy_zc = partial_correlation_recursive(
+ new_xdata, new_ydata, zc, method=method,
+ omit_nones=omit_nones)
+ rxz0_zc = partial_correlation_recursive(
+ new_xdata, tuple(data["z0"]), zc, method=method,
+ omit_nones=omit_nones)
+ ryz0_zc = partial_correlation_recursive(
+ new_ydata, tuple(data["z0"]), zc, method=method,
+ omit_nones=omit_nones)
+
+ return round(
+ ((rxy_zc - rxz0_zc * ryz0_zc) /(
+ math.sqrt(1 - rxz0_zc**2) * math.sqrt(1 - ryz0_zc**2))),
+ ROUND_TO)