SuSiE-RSS UKB (using 3 steps)

Last updated: 2021-03-16

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Knit directory: dsc_susierss/

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Rmd	9b772ae	zouyuxin	2021-03-16	update results

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 1000 samples to get reference LD matrix. We simulate data with 1,2,3 signals and PVE 0.005. We run susie_rss with L=10 using the 3 steps procudure. We run FINEMAPv1.1 and CAVIAR with oracle number of signals. We run FINEMAPv1.4 with oracle number of signals and max 4 signals.

We first check the impact of estimating residual variance.