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| author | Frederick Muriuki Muriithi | 2021-11-04 08:51:50 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-11-04 12:45:57 +0300 |
| commit | 78c1d118ca31e2c0d4cd12afe8c8426974ee82e2 (patch) | |
| tree | 112dfc81303a747f23ba7f4a17f7cfe61ee20a1e /gn3 | |
| parent | 75d2286185addb3953f728d5fc30d2fd13ffbaf0 (diff) | |
| download | genenetwork3-78c1d118ca31e2c0d4cd12afe8c8426974ee82e2.tar.gz | |
Create blackbox tests for some functions migrated from R
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: new stub
functions (partial_correlation_matrix, partial_correlation_recursive)
*
tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv:
blackbox sample data and results for variance-covariance matrix method
*
tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv:
blackbox sample data and results for recursive method
* tests/unit/computations/test_partial_correlations.py: Tests for new function
Provide some blackbox testing sample data for checking the operation of the
functions migrated from R.
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index fb372a9..07dc16d 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -257,3 +257,33 @@ def compute_partial_correlations_fast(# pylint: disable=[R0913, R0914] (fetched_correlations[corr[0]],) if correlation_type == "literature" else fetched_correlations[corr[0]][0:2]) for idx, corr in enumerate(all_correlations)) + +def partial_correlation_matrix( + xdata: Tuple[float, ...], ydata: Tuple[float, ...], + zdata: Tuple[float, ...], method: str = "pearsons", + omit_nones: bool = True) -> float: + """ + Computes the partial correlation coefficient using the + 'variance-covariance matrix' method + + This is a partial migration of the + `web.webqtl.correlation.correlationFunction.determinPartialsByR` function in + GeneNetwork1, specifically the `pcor.mat` function written in the R + programming language. + """ + return 0 + +def partial_correlation_recursive( + xdata: Tuple[float, ...], ydata: Tuple[float, ...], + zdata: Tuple[float, ...], method: str = "pearsons", + omit_nones: bool = True) -> float: + """ + Computes the partial correlation coefficient using the 'recursive formula' + method + + This is a partial migration of the + `web.webqtl.correlation.correlationFunction.determinPartialsByR` function in + GeneNetwork1, specifically the `pcor.rec` function written in the R + programming language. + """ + return 0 |