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Performance of MCMC. (a) Autocorrelation plot obtained by running BEAM2 on a simulated data set of 1,000 cases, 1,000 controls, and 1,000 SNPs under disease Model 2. A total of 1,000 iterations after burn-in are used to calculate the plot. (b) Posterior probabilities (in logarithm scale) of disease association (marginal and epistatic) per SNP compared across 4 independent runs of BEAM2.
