setClassUnion("characterOrNULL", c("character", "NULL"))
#' Multi Omics Modules.
#'
#' This class organize the results of the Multi Omics Module Survival Test analysis.
#'
#' @slot alphas numeric vector of the pvalues of all the modules.
#' @slot zlists a list of all the zs of the covariates.
#' @slot coxObjs a list with all the data.frame used for coxph of each module.
#' @slot modulesView a list of module information: for each omic the module data, the method used and the covariate analyzed.
#' @slot modules a list woth the genes that belong to the module.
#' @slot formulas a list, for each module the character of the formula used in the coxph.
#' @slot graphNEL the graphNEL version of the pathway used in the analysis.
#' @slot title the name of the pathway.
#'
setClass("MultiOmicsModules", package = "MOSClip",
slots = c(alphas = "numeric",
zlists = "list",
coxObjs = "list",
modulesView = "list",
modules = "list",
formulas = "list",
graphNEL = "graphNEL",
title = "characterOrNULL"))
setMethod("show",
signature = "MultiOmicsModules",
definition = function(object) {
sthis <- seq_len(min(length(object@alphas), 3))
sthis <- order(object@alphas)[sthis]
sigCliquesIdx = which(object@alphas <= 0.05)
if (!is.null(object@title)) {
cat("\"",object@title, "\"\n", sep = "")
}
for (i in sthis) {
cat(paste0("Module ",i, ": pvalue ", object@alphas[i], "\n"))
covs <- names(which(object@zlists[[i]] <=0.05))
if (length(covs)!=0)
cat("The following covariates are implicated:\n",paste(covs, collapse=", "),"\n")
cat("Module is composed by the followings:\n")
cat(paste(object@modules[[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)
})
#' Multi Omics Pathway.
#'
#' This class organize the results of the Multi Omics Module Survival Test analysis.
#'
#' @slot pvalue numeric, the pvalues of the whole module.
#' @slot zlist a vector of all the zs of the covariates.
#' @slot coxObj a data.frame used for the coxph model.
#' @slot pathView a list, for each omic the pathway data, the method used and the covariate analyzed.
#' @slot formulas a list, for each module the character of the formula used in the coxph.
#' @slot graphNEL the graphNEL version of the pathway used in the analysis.
#' @slot title the name of the pathway.
#'
#' @name MultiOmicsPathway-class
#' @rdname MultiOmicsPathway-class
#'
setClass("MultiOmicsPathway", package = "MOSClip",
slots = c(pvalue = "numeric",
zlist = "numeric",
coxObj = "data.frame",
pathView = "list",
formula = "character",
graphNEL = "graphNEL",
title = "characterOrNULL"))
setMethod("show",
signature = "MultiOmicsPathway",
definition = function(object) {
if (!is.null(object@title)) {
cat("\"",object@title, "\"\n", sep = "")
}
cat(paste0("Pathway overall pvalue: ", object@pvalue, "\n"))
invisible(NULL)
})
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