Cross-GWAS coherence test at the gene and pathway level
Fig 2
QQ-plots of observed p-values resulting from the index I for 1000 pairs of samples of against uniform p-values.
A: Off-diagonal elements of Σ set to 0.2. B: Off-diagonal set to 0.8. The blue curve is obtained using the variance-gamma distribution to perform the statistical test, while the orange curve is obtained via the weighted χ2 distribution. The latter corrects for the correlation and therefore is well calibrated.