Example 2: RSS-BVSR with Various LD Matrices

Last updated: 2024-07-03

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Overview

This example illustrates the impact of different LD estimates on the RSS results. Three types of estimated LD matrices are considered: cohort sample LD, panel sample LD and shrinkage panel sample LD in Wen and Stephens, (2010) This example is closely related to Section 4.1 of Zhu and Stephens (2017).

The single-SNP summary-level data are computed from a simulated GWAS dataset. The simulation scheme is described in Section 4.1 Zhu and Stephens (2017). Specifically, 10 “causal” SNPs are randomly drawn from 982 SNPs on chromosome 16, with effect sizes coming from standard normal \({\cal N}(0,1)\). Effect sizes of remaining SNPs are zero. The true PVE (SNP heritability) is 0.2.

Three types of LD estimates are considered here.

cohort sample LD: the sample correlation matrix using genotypes in the cohort (WTCCC UK Blood Service Control Group)
shrinkage panel sample LD: the shrinkage correlation matrix (Wen and Stephens, 2010) using genotypes in the panel (WTCCC 1958 British Birth Cohort)
panel sample LD: the sample correlation matrix using genotypes in the panel (WTCCC 1958 British Birth Cohort)

To reproduce results of Example 2, please read the step-by-step guide below and run example2.m. Before running example2.m, please first install the MCMC subroutines. Please find installation instructions here.

Step-by-step illustration

Step 1. Download data files.

All data files required to run this example are freely available at Zenodo . Please contact me if you have trouble accessing this file. After a complete download, you should see the following files.

$ tree ./
./
├── example2.mat
└── readme

0 directories, 2 files

The data file example2.mat contains the following elements.

betahat: 982 by 1 vector, single-SNP effect size estimate for each SNP
se: 982 by 1 vector, standard errors of the single-SNP effect size estimates
Nsnp: 982 by 1 vector, sample size of each SNP
cohort_R: cohort sample LD
shrink_R: shrinkage panel sample LD
panel_R: panel sample LD
snp_info: 3 by 1 cell, ID and allele of each SNP

Step 2. Fit three RSS-BVSR models with different LD matrices.

% cohort sample LD
[betasam, gammasam, hsam, logpisam, Naccept] = rss_bvsr(betahat, se, cohort_R, Nsnp, Ndraw, Nburn, Nthin);

% shrinkage panel sample LD
[betasam, gammasam, hsam, logpisam, Naccept] = rss_bvsr(betahat, se, shrink_R, Nsnp, Ndraw, Nburn, Nthin);

% panel sample LD
[betasam, gammasam, hsam, logpisam, Naccept] = rss_bvsr(betahat, se, panel_R, Nsnp, Ndraw, Nburn, Nthin);

More simulations

The simulations in Section 4.1 of Zhu and Stephens (2017) are essentially “replications” of the example above. The simulated datasets in Section 4.1 are available as rss_example2_data_{1/2/3}.tar.gz¹.

Each simulated dataset contains three files: genotype.txt, phenotype.txt and simulated_data.mat. The files genotype.txt and phenotype.txt are the genotype and phenotype files for GEMMA. The file simulated_data.mat contains three cells.

true_para = {pve, beta, gamma, sigma};
individual_data = {y, X};
summary_data = {betahat, se, Nsnp};

Only the summary_data cell above is used as the input for RSS methods.

RSS methods also require an estimated LD matrix. The three types of LD matrices are provided in the file genotype2.mat¹.

After applying RSS methods to these simulated data, we obtain the following results.

True PVE = 0.2

True PVE = 0.02	True PVE = 0.002

Footnotes:

Currently these files are locked, since they contain individual-level genotypes from Wellcome Trust Case Control Consortium (WTCCC, https://www.wtccc.org.uk/). You need to get permission from WTCCC before we can share these files with you.

devtools::session_info()

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Example 2: RSS-BVSR with Various LD Matrices

Xiang Zhu

Overview

Step-by-step illustration

More simulations