Fine Mapping Causal Variants with an Approximate Bayesian Method Using Marginal Test Statistics

Supporting Information

Supporting Information

  • Supporting Information - File S1, Table S1, and Figures S1-S13 (PDF, 1 MB)
  • File S1 - Approximate equivalence between BIMBAM and CAVIAR for binary traits and non-centrality parameters of the marginal test statistics under multiple causal SNPs. (PDF, 474 KB)
  • Table S1 - Average number of SNPs needed to include 50% and 90% causal SNPs among 100 simulated data sets under different number of causal SNPs for binary trait. (PDF, 89 KB)
  • Figure S1 - Comparison of different fine mapping methods on binary traits. (PDF, 56 KB)
  • Figure S2 - Comparison of different prior values σa on binary traits. (PDF, 70 KB)
  • Figure S3 - Comparison of different criteria to prioritize variants on binary traits. (PDF, 63 KB)
  • Figure S4 - Estimated probabilities of ρ-level confidence set and boxplots of the number of selected SNPs. (PDF, 70 KB)
  • Figure S5 - Estimated probabilities of ρ-level confidence set and boxplots of the number of selected SNPs for independent SNPs. (PDF, 70 KB)
  • Figure S6 - P-values and posterior inclusion probabilities (PIPs) for independent SNPs. (PDF, 24 KB)
  • Figure S7 - Calibration of the posterior inclusion probabilities (PIPs) on binary traits. (PDF, 49 KB)
  • Figure S8 - P-values and posterior inclusion probabilities (PIPs) from BIMBAM on U.S. cohort. (PDF, 161 KB)
  • Figure S9 - P-values and posterior inclusion probabilities (PIPs) from PAINTOR on U.S. cohort. (PDF, 161 KB)
  • Figure S10 - P-values and posterior inclusion probabilities (PIPs) from CAVIARBF on San Diego cohort. (PDF, 203 KB)
  • Figure S11 - P-values and posterior inclusion probabilities (PIPs) from BIMBAM on San Diego cohort. (PDF, 203 KB)
  • Figure S12 - P-values and posterior inclusion probabilities (PIPs) from PAINTOR on San Diego cohort. (PDF, 203 KB)
  • Figure S13 - P-values and posterior inclusion probabilities (PIPs) from CAVIARBF on U.S. cohort using estimated correlation matrix from EUR population in the 1000 Genomes Project. (PDF, 161 KB)