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Add Cochran-Mantel-Haenszel statistical test for association

Open Will-Tyler opened this issue 4 months ago • 5 comments

Description

In this pull request, I add a function to perform a Cochran-Mantel-Haenszel statistical test for association.

This pull request closes #13481.

Testing

I add unit tests. Since I have not used R before (the associated GitHub issue suggests using R to create test cases), I created the unit tests from examples that I found on the internet. I linked these sources in the code for the unit tests.

I built the documentation locally and inspected it to confirm that it matches my expectations.

I am having trouble testing the docstring examples locally. When I run make -C hail doctest-query, the tests error due to a checksum exception.

Discussion

~I have not added an example to the documentation that uses a matrix table yet. (This is an acceptance criteria in #13481.) I wanted to get some advice about the best way to do this. I think ideally, the example would have a binary phenotype, an allele to test for association, and some stratifying variable. I tried to search through the existing code to find suitable example matrix tables in the docstrings, but I didn't find anything promising. I would appreciate help here.~

Update: thanks to @patrick-schultz's recommendation, I have added an example using a matrix table.

Will-Tyler avatar Feb 06 '24 05:02 Will-Tyler