Table 1.
Interpretation of parameter values in the fitted model. Parameters τ, σ2 and σ3 are dependent on sample sizes, but can be converted to sample-size independent forms (see supplementary note)
| Model | Interpretation | |
|---|---|---|
| π1 | H0 / H1 | Proportion of SNPs not associated with case/control (category 1) |
| π2 | H0 / H1 | Proportion of SNPs associated with case/control status but not subgroup status (category 2) |
| π3 | H0 / H1 | Proportion of SNPs associated with subgroup status (category 3) |
| τ | H0 / H1 | Standard deviation of observed Zd scores (effect sizes for subgroup status) in category 3 |
| σ2 | H0 / H1 | Standard deviation of observed Za scores (effect sizes for case/control status) in category 2 |
| σ3 | H1 only | Standard deviation of observed Za scores (effect sizes for case/control status) in category 3 |
| ρ | H1 only | ‘Absolute covariance’ between Zd scores (effect sizes for subgroup status) and Za scores (effect sizes for case/control status) in category 3 |