minP: minP.R

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

Description

Given a vector of individual test statistics and their pairwise correlations, calculate the MinimumP (see Conneely and Boehnke, 2007) second-level test statistic and it's p-value.

Usage

minP(test_stats, cor_mat = NULL, pairwise_cors = NULL)

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. You only need to specify EITHER cor_mat OR pairwise_cors.
pairwise_cors	A vector of all d(d-1)/2 pairwise correlations between the test statistics. You only need to specify EITHER cor_mat OR pairwise_cors.

Value

A list with the elements:

minP	The observed MinimumP test statistic.
minP_pvalue	The p-value of this observed value, given the size of the set and correlation structure.

Examples

# Should return statistic = 0.05918928 and p_value = 0.2525972.
set.seed(100)
Z_vec <- rnorm(5) + rep(1,5)
cor_Z <- matrix(data=0.2, nrow=5, ncol=5)
diag(cor_Z) <- 1
minP(test_stats=Z_vec, cor_mat=cor_Z)

Example output

$minP
[1] 0.05918928

$minP_pvalue
[1] 0.2525972

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