Examples

We illustrate how to use RSS software through the following examples.

• Example 1: Fit the RSS models via MCMC, and estimate the SNP heritability (PVE).

This example illustrates how to fit RSS models using MCMC algorithms. Three types of prior distributions are considered: BVSR, BSLMM and ASH. The output of MCMC is further used to estimate the SNP heritability.

• Example 2: Fit RSS-BVSR via MCMC with three types of LD matrices.

This example illustrates the impact of different LD estimates on the RSS results. Three types of estimated LD matrices are considered: cohort sample LD, shrinkage panel sample LD (Wen and Stephens 2010) and panel sample LD.

• Example 3: Fit RSS-BVSR via MCMC with two types of SE vectors.

This example illustrates the impact of two definitions of se on the RSS results.

• Example 4: Fit RSS-BVSR via variational Bayes (VB) methods.

This example illustrates how to fit an RSS-BVSR model using variational Bayes (VB) approximation, compare the results with previous work based on individual-level data (Carbonetto and Stephens, 2012).