R/Stouffer.test.R

In metaSeq: Meta-analysis of RNA-Seq count data in multiple studies

Stouffer.test <-
function (pvals, na.mode = "notignore") 
{
    if (is.null(pvals["weight", ][[1]])) {
        stop("Weight is needed for Stouffer's method!\n")
    }
    else {
        l <- ncol(pvals)
        U <- pvals[1, 1][[1]]
        L <- pvals[2, 1][[1]]
        weight <- unlist(pvals["weight", ])
        for (i in 2:l) {
            U <- cbind(U, pvals[1, i][[1]])
            L <- cbind(L, pvals[2, i][[1]])
        }
        up <- c()
        low <- c()
        if (na.mode == "notignore") {
            up <- apply(U, 1, each.Stouffer.test, w = weight)
            low <- apply(L, 1, each.Stouffer.test, w = weight)
        }
        else if (na.mode == "ignore") {
            up <- apply(U, 1, each.Stouffer.ignore.test, w = weight)
            low <- apply(L, 1, each.Stouffer.ignore.test, w = weight)
        }
        else {
            warnings("You have to specify na.mode as \"ignore\" or \"notignore\"")
        }
        list(Upper = up, Lower = low, Weight = weight)
    }
}