estimate_ss_cor: estimate_ss_cor.R

In GBJ: Generalized Berk-Jones Test for Set-Based Inference in Genetic Association Studies

estimate_ss_cor.R

Description

Estimate the correlations between GWAS summary statistics using reference panel eigenvectors and reference panel genotypes.

Usage

estimate_ss_cor(ref_pcs, ref_genotypes, link_function)

Arguments

ref_pcs	An n*m matrix containing PCs calculated from the reference panel. Here n is the number of subjects in the reference panel and m is roughly the number of PCs used in the original analysis which produced the summary statistics.
ref_genotypes	An n*d matrix holding the genotypes from the reference panel, where the d columns correspond to the d SNPs for which we have summary statistics. No missing data allowed.
link_function	Either "linear" or "logit" or "log".

Value

A list with the elements:

cor_mat

The d*d matrix giving the pairwise correlation of every two test statistics.

Examples

ref_pcs <- matrix(data=runif(n=1000, min=-0.2, max=0.2), ncol=5)
ref_genotypes <- matrix(data=rbinom(n=2000, size=2, prob=0.3), ncol=10)
estimate_ss_cor(ref_pcs=ref_pcs, ref_genotypes=ref_genotypes, link_function="linear")

GBJ documentation built on May 29, 2024, 1:33 a.m.