EMPIRICAL COVERAGE: Average coverage from simulations (“true coverage”)

CLAIMED COVERAGE: Size of the credible set

CORRECTED COVERAGE: GAM predicted coverage

Empirical and Claimed Coverage Plots From Simulations Using Real-World Data

(Wrong) Simulation method:

  1. Obtain freq, a reference haplotype matrix based on real world MAF and LD data.

  2. For a fixed OR (odds ratio) and N (sample size), generate nrep (=100) posterior probability systems.
  3. For each of these, form two credible sets: one using ordered posterior probabilities and one using unordered posterior probabilities. Obtain the size (claimed coverage) and whether the CV is in the set for each credible set (covered). The same CV is chosen as causal for these systems.
  4. In the form a table, report: order (whether the posterior probabilities were ordered), threshold, size, nvar (number of variants in the credible set), covered (whether the CV was in the credible set), N (sample size) and OR.
  5. Replicate steps 2-4 many times for varying thresholds (0.6, 0.8, 0.9, 0.95) ORs (1.001, 1.05, 1.1, 1.15, 1.2, 1.25, 1.3) and sample sizes (N0=N1=2000, 5000, 10000, 50000).