R/global.Pearson.R

In safe: Significance Analysis of Function and Expression

global.Pearson <-
function (C.mat, u, args.global)
{
    if (is.null(args.global$genelist.cutoff)) {
        stop("args.global$genelist.cutoff must be specified",
            call. = FALSE)
    }
    m2 <- length(u)
    size2 <- (rep(1, m2) %*% C.mat)[1, ]
    if (!args.global$one.sided) {
        return(function(u, C.mat2 = C.mat, cut = args.global$genelist.cutoff,
            size = size2, m = m2) {
            o1 <- (t(C.mat2) %*% as.numeric(abs(u) >= cut))
            o2 <- sum(abs(u) >= cut) - o1
            diff <- (o1/size - o2/(m - size))/sqrt((o1 + o2) *
                (1 - o1/m - o2/m)/size/(m - size))
            return(as.numeric(diff))
        })
    }
    else {
        return(function(u, C.mat2 = C.mat, cut = args.global$genelist.cutoff,
            size = size2, m = m2) {
            o1 <- (t(C.mat2) %*% as.numeric(u >= cut))
            o2 <- sum(u >= cut) - o1
            diff <- (o1/size - o2/(m - size))/sqrt((o1 + o2) *
                (1 - o1/m - o2/m)/size/(m - size))
            return(as.numeric(diff))
        })
    }
}