Nothing
survCliques <- setClass("survCliques", package = "survClip",
slots = c(alphas = "numeric",
zlist = "list",
cliques = "list",
coxObjs = "list",
cliquesLoadings = "list",
cliquesExpr = "list"),
contains = "list"
)
setMethod("show",
signature = "survCliques",
definition = function(object) {
sthis <- seq_len(min(length(object@alphas), 3))
sthis <- order(object@alphas)[sthis]
sigCliquesIdx = which(object@alphas <= 0.05)
for (i in sthis) {
cat(paste0("Cliques ",i, ": pvalue ", object@alphas[i], "\n"))
cat("Clique is composed by the followings:\n")
cat(paste(object@cliques[[i]], collapse=", "))
cat("\n-+-\n")
}
if (length(sthis) < length(sigCliquesIdx)) {
cat(paste0("There are other ", length(sigCliquesIdx)-length(sthis), " cliques with pvalue <= 0.05"))
}
invisible(NULL)
})
survPath <- setClass("survPath", package = "survClip",
slots = c(pvalue = "numeric",
zlist = "numeric",
coxObj = "data.frame",
loadings = "matrix",
method = "character"),
contains = "list"
)
setMethod("show",
signature = "survPath",
definition = function(object) {
cat(paste0("Pathway processed with ", object@method, " method\n pvalue: ", object@pvalue, "\n"))
invisible(NULL)
})
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