Last updated: 2021-09-17

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This simulation uses UKB genotype data. We extract the genotype regions based on height GWAS result. There are 200 regions, each with ~1000 SNPs. We sample 50,000 individuals to simulate the data. We sample another 500 and 1000 samples to get reference LD matrix. We simulate data with 1,2,3 signals and PVE 0.005. We run susie_rss using L=10. We run FINEMAP v1.4 with oracle number of signals and max 4 signals. We run CAVIAR with oracle number of signals. We run DAP-G with the default setting.

Power vs FDR

SuSiE-suff with refinement vs no refinement

Different methods with in sample LD

Different methods with in sample LD

Different methods with LD ref1000 with \(\lambda = 0\)

Different methods with LD ref1000 with \(\lambda = 0.001\)

Different methods with LD ref1000 with \(\hat{\lambda}\)

Different methods with LD ref500 with \(\lambda = 0\)

Different methods with LD ref500 with \(\lambda = 0.001\)

Different methods with LD ref500 with \(\hat{\lambda}\)

CAVIAR under different LD

FINEMAP-oracle under different LD

FINEMAP-L4 under different LD

DAP-G under different LD

SuSiE-RSS L = oracle under different LD

SuSiE-RSS L = 10 under different LD

CS