R/gates.R

In COMBAT: A Combined Association Test for Genes using Summary Statistics

# Function of GATES
gates = function(x, cor_G){
	if(is.positive.definite(cor_G)==FALSE) stop('cor_G is not positive definite. Please re-calculate with ld.Rsquare function.\n')
	pval_sort  <- sort(x)
	pval_order <- order(x)
	n_snps     <- length(x)

	cor_P <- cor_G[pval_order, pval_order]
	cor_P <- 0.2982*cor_P^6 - 0.0127*cor_P^5 + 0.0588*cor_P^4 + 0.0099*cor_P^3 + 0.6281*cor_P^2 - 0.0009*cor_P
        
	p_gates <- ext_simes(pval_sort, cor_P)
	p_gates
}