Nothing
setClass("hommel",
representation(
p = "numeric", #(m) store vector of p-values (possibly with names)
jumpalpha = "numeric", #(m+1) stores vector of alphas where h(alpha) jumps
sorter = "integer", #(m) permutation to sort p
adjusted = "numeric", #(m) stores adjusted p-values
simesfactor = "numeric", #(m+1) stores simesfactor (start at 0)
simes = "logical" # stores whether adjusted p-values ar calculated based on a Simes test (if TRUE) or on Hommel's test from 1983 (if FALSE)
)
)
setMethod("p.adjust", "hommel", function(p, method, n) {
if(!missing(method)) {
if (p@simes)
method = "Hommel's method (Simes inequality assumed)"
else
method = "Hommel's method (Simes inequality not assumed)"
stop(paste("Method argument not used. Method is", method))
}
if (!missing(n)) {
stop("argument n not used.")
}
p@adjusted
})
setMethod("show", "hommel", function(object) {
cat("A hommel object for", length(object@p), "hypotheses.\n")
if (object@simes)
cat("Simes inequality is assumed.\n")
else
cat("Simes inequality is not assumed.\n")
cat("Use p.adjust(), discoveries() or localtest() to access this object.\n")
})
setMethod("summary", "hommel", function(object, alpha = 0.05, ...) {
show(object)
cat("\n")
disc <- discoveries(object, alpha=alpha)
cat("With", 1-alpha, "confidence: at least", sum(disc), "discoveries.\n")
cat(sum(object@adjusted <= alpha), " hypotheses with adjusted p-values below ", alpha, ".\n", sep="")
})
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