OMNI_ss: omni_ss.R

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

Description

Computes the omnibus test statistic combining GBJ, GHC, minP, and SKAT. This version of the function assumes you are using GWAS summary statistics. If you individual-level genotype data, use omni_individual().

Usage

OMNI_ss(test_stats, cor_mat, num_boots = 100)

Arguments

test_stats	Vector of test statistics for each factor in the set (i.e. marginal test statistic for each SNP in a gene)
cor_mat	d*d matrix of the correlations between all the test statistics in the set, where d is the total number of test statistics in the set.
num_boots	Number of bootstrap repetitions to find correlation matrix of set-based statistics.

Value

A list with the elements:

OMNI	The observed omnibus test statistic.
OMNI_pvalue	The p-value of the OMNI test
err_code	Sometimes if your p-value is very small (< 1*10^(-10)), R may run into numerical issues. This message will alert you if such a situation occurs.

Examples

cor_mat <- matrix(data=0.3, nrow=5, ncol=5)
diag(cor_mat) <- 1
test_stats <- as.numeric(mvtnorm::rmvnorm(n=1, sigma=cor_mat))
OMNI_ss(test_stats=test_stats, cor_mat=cor_mat, num_boots=5)

GBJ documentation built on March 26, 2020, 6:05 p.m.