R/ExprData-class.R

In jcrodriguez1989/MIGSA: Massive and Integrative Gene Set Analysis

#' ExprData S4 class implementation in R
#'
#' This S4 class contains the expression data, it can be a MAList or DGEList.
#' Important: Rownames are going to be used as gene identifiers, make sure that
#' this IDs are the same used in your gene sets.
#'
#' @docType methods
#' @name ExprData-class
#' @rdname ExprData-class
#'
#' @importClassesFrom edgeR DGEList
#' @importClassesFrom limma MAList
#' @exportClass ExprData
#' @examples
#' ## Lets create a ExprData object from counts data (DGEList).
#' rnaData <- matrix(rnbinom(10000, mu = 5, size = 2), ncol = 4)
#' rownames(rnaData) <- 1:nrow(rnaData)
#' # It must have rownames (gene names).
#'
#' ## Now we can use rnaExprData as an ExprData object.
#' \dontrun{
#' rnaExprData <- DGEList(counts = rnaData)
#' }
#'
#' ## Lets create a ExprData object from micro array data (MAList).
#' maData <- matrix(rnorm(10000), ncol = 4)
#' rownames(maData) <- 1:nrow(maData)
#' # It must have rownames (gene names).
#'
#' ## Now we can use maExprData as an ExprData object.
#' maExprData <- new("MAList", list(M = maData))
setClassUnion("ExprData", c("MAList", "DGEList"))