Extended Data Fig. 3: Additional evidence of performance improvements in real data.
From: Improving fine-mapping by modeling infinitesimal effects
a-b. Functional enrichment of top N (N = 500, 1000, 1500, and 3000) highest PIP variants from SuSiE, SuSiE-inf, FINEMAP, and FINEMAP-inf. GWAS summary statistics computed using BOLT-LMM and OLS. c. Functional enrichment of the set differences between SuSiE and SuSiE-inf high-PIP (PIP > 0.9) variants and FINEMAP and FINEMAP-inf high-PIP variants. Error bars represent one SD of the corresponding binomial distribution Binom(n,p), where n is the total number of variants in each set and p is the corresponding proportion of annotated variants). Bar plot data is presented as proportion +/- SD. d. The proportion of reduction for the number of variants in three categories when using the SuSiE-inf and FINEMAP-inf compared to using SuSiE and FINEMAP. The three categories are: High-PIP (PIP > 0.9 for either method, reduced from 1876 to 1578), Replicated (PIP > 0.9 at both sample sizes N = 100 K and N = 366 K, reduced from 665 to 595), and Shared high-PIP (PIP > 0.9 for both method, reduced from 723 to 646). e. Credible set sizes in all regions fine-mapped by SuSiE and SuSiE-inf. 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. Numerical results available in Supplementary Table 16-20.
