Math behind association with PLINK
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The most basic association test is just a Chi-squared test on a 2 x 2 contingency table of the minor allele tallies, as to which I elaborate here: A: SNP dataset and Z Score
Any other test, such as linear / logistic regression, family-based tests, etc., are a mixture of again using minor allele tallies or genotypes encoded categorically (
HOM) with different assumptions about inheritance patterns.
Perhaps focus on the mathematics of these specific tests outside of PLINK as opposed to finding the exact formulae within the PLINK documentation itself. PLINK just re-uses already-published statistical tests.
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