R/SKAT_Optimal_Integrate_Func_Davies.R

In KMgene: Gene-Based Association Analysis for Complex Traits

#' @importFrom stats dchisq

SKAT_Optimal_Integrate_Func_Davies <- function (x, pmin.q, param.m, r.all, acc)
 {
    n.r <- length(r.all)
    n.x <- length(x)
    temp1 <- param.m$tau %x% t(x)
    temp <- (pmin.q - temp1)/(1 - r.all)
    temp.min <- apply(temp, 2, min)
    re <- rep(0, length(x))
    for (i in 1:length(x)) {
        min1 <- temp.min[i]
        if (min1 > sum(param.m$lambda) * 10^4) {
            temp <- 0
        }
        else {
            min1.temp <- min1 - param.m$MuQ
            sd1 <- sqrt(param.m$VarQ - param.m$VarRemain)/sqrt(param.m$VarQ)
            min1.st <- min1.temp * sd1 + param.m$MuQ
            dav.re <- davies(min1.st, param.m$lambda, acc=acc)
            temp <- dav.re$Qq
            if (dav.re$ifault != 0) {
                stop("dav.re$ifault is not 0")
            }
        }
        if (temp > 1) {
            temp = 1
        }
        re[i] <- (1 - temp) * dchisq(x[i], df = 1)
    }
    return(re)
 }