#' S4 class union data.frame_OR_EList

#'

#' @description Virtual class union containing members of \code{data.frame} and

#'  \code{limma::Elist}, used internally to handle situations when a returned

#'  object has a type that cannot be guessed from the function call.

#'

#' @return fusion of classes \code{data.frame} and \code{EList}, used within

#'  \code{.biotmle} by class \code{bioTMLE} to handle uncertainty in the object

#'  passed to slot "tmleOut".

#'

#' @importFrom methods setClassUnion new

#' @importClassesFrom methods data.frame

#' @importClassesFrom limma EList

#' @importClassesFrom S4Vectors Vector Annotated

#'

#' @export

setClassUnion(

  name = "data.frame_OR_EList",

  members = c("data.frame", "EList")

)

###############################################################################

#' Constructor for class bioTMLE

#'

#' @return class \code{biotmle} object, sub-classed from SummarizedExperiment.

#'

#' @import BiocGenerics

#' @importClassesFrom SummarizedExperiment SummarizedExperiment

#' @importFrom methods setClass

#'

#' @export .biotmle

#' @exportClass bioTMLE

#'

#' @rdname bioTMLE-class

#'

#' @examples

#' library(SummarizedExperiment)

#' library(biotmleData)

#' data(illuminaData)

#'

#' example_biotmle_class <- function(se) {

#'   call <- match.call(expand.dots = TRUE)

#'   biotmle <- .biotmle(

#'     SummarizedExperiment(

#'       assays = assay(se),

#'       rowData = rowData(se),

#'       colData = colData(se)

#'     ),

#'     call = call,

#'     ateOut = as.numeric(rep(NA, 10)),

#'     tmleOut = as.data.frame(matrix(NA, 10, 10)),

#'     topTable = as.data.frame(matrix(NA, 10, 10))

#'   )

#'   return(biotmle)

#' }

#'

#' example_class <- example_biotmle_class(se = illuminaData)

.biotmle <- methods::setClass(

  Class = "bioTMLE",

  slots = list(

    call = "call",

    ateOut = "vector",

    tmleOut = "data.frame_OR_EList",

    topTable = "data.frame"

  ),

  contains = "SummarizedExperiment"

)

###############################################################################

#' Accessor for Table of Raw Efficient Influence Function Values

#'

#' @param object S4 object of class \code{bioTMLE}.

#'

#' @importFrom methods is

#' @importFrom assertthat assert_that

#'

#' @return contents of \code{tmleOut} slot of object of class \code{biotmle}.

#'

#' @export

eif <- function(object) {

  assertthat::assert_that(is(object, "bioTMLE"))

  object@tmleOut

}

###############################################################################

#' Accessor for Results of Moderated Influence Function Hypothesis Testing

#'

#' @param object S4 object of class \code{bioTMLE}.

#'

#' @importFrom methods is

#' @importFrom assertthat assert_that

#'

#' @return contents of \code{topTable} slot of object of class \code{biotmle}.

#'

#' @export

toptable <- function(object) {

  assertthat::assert_that(is(object, "bioTMLE"))

  object@topTable

}