= LOD score
{c}
{title2=$Z(\theta)=\log_{10}[L(\theta)/L(1/2)]$}
The LOD score compares the likelihood at recombination fraction $\theta$ with independent assortment:
$$
Z(\theta)=\log_{10}\frac{L(\theta)}{L(1/2)}.
$$
When phenotype likelihood is independent of $\theta$, it can be computed from marker probabilities conditional on phenotype and ascertainment. Positive values support linkage; the observed marker pattern must be specified precisely because affected-only and affected-plus-unaffected observations give different likelihoods.
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