Extended Data Fig. 5: Estimated infinitesimal variance (tau squared) in UK Biobank.
From: Improving fine-mapping by modeling infinitesimal effects
a. Estimated tau squared in all fine-mapped regions for 10 UK Biobank phenotypes at sample size N = 366 K. Box plot lower and upper hinges correspond to 1st and 3rd quantiles, whiskers extend no further than 1.5*IQR from the hinges, outliers are plotted as individual points, solid line in the boxes show medians and the red dot denotes the mean. b. Comparing mean tau-squared estimates between traits. Heatmap shows the results of pair-wise Welch two-sample T-test with alternative hypothesis: mean of estimated tau squared in all regions for trait 1 (x-axis) is greater than that of trait 2 (y-axis). The test is one-sided. Multiple-testing adjusted p-value significance cutoff is set to be 0.05/90 = 5.5e-4, correcting for the total number of trait pairs tested. Stars indicate p-value has passed the significant threshold. c. Correlation between number of credible sets and the estimated infinitesimal variance (tau squared). Regions with the same number of credible sets are aggregated, and the median estimated tau squared are obtained from these regions. Scatter plot shows these medians. The best fitted line is plotted using ggscatter. R is the Pearson correlation, and p is the two-sided correlation p-value. The 95% confidence interval is shown on the plot as the gray shaded area. Numerical results available in Supplementary Table 24-26.
