R/error.FDR.YB.R

In safe: Significance Analysis of Function and Expression

error.FDR.YB <-
function (P.matrix) {
    order <- order(order(P.matrix[1, ]))
    P.matrix <- P.matrix[, order(P.matrix[1, ])]
    num.perms <- dim(P.matrix)[[1]]
    num.cat <- dim(P.matrix)[[2]]
    s.hat <- rep(NA, num.cat)
    YB <- rep(NA, num.cat)
    YB.funct <- function(k.vec, p, s) {
        v.k <- sum(k.vec <= p)
        if ((v.k + s) > 0)
            return(v.k/(v.k + s))
        else return(0)
    }
    for (i in 1:num.cat) {
        s.hat[i] <- max(0, sum(P.matrix[1, ] <= P.matrix[1, i]) -
            sum(P.matrix[-1, ] <= P.matrix[1, i])/(num.perms -
                1))
        YB[i] <- mean(apply(P.matrix[-1, ], 1, YB.funct, P.matrix[1,
            i], s.hat[i]))
    }
    for (i in (num.cat - 1):1) YB[i] <- min(YB[i], YB[i + 1])
    return(YB[order])
}