R/ACATO.R

In sumFREGAT: Fast Region-Based Association Tests on Summary Statistics

# ACAT function by Yaowu Liu, with changes

ACATO <- function(p){
    if (all(is.na(p))) return(NA)
    p <- p[!is.na(p)]
    p[p == 1] <- 1 - 1e-16
#### check if there are very small non-zero p values
    is.small <- (p < 1e-16)
    if (sum(is.small) == 0) {
        cct.stat <- sum(tan((0.5 - p) * pi))/length(p)
    } else {
        cct.stat <- sum((1 / p[is.small]) / pi)
        cct.stat <- cct.stat + sum(tan((0.5 - p[!is.small]) * pi))
        cct.stat <- cct.stat/length(p)
    }
    #### check if the test statistic is very large.
    if (cct.stat > 1e+15){
        pval <- (1 / cct.stat) / pi
    } else {
        pval <- 1 - pcauchy(cct.stat)
    }
    pval
}