R/SEAparams-class.R

In jcrodriguez1989/MIGSA: Massive and Integrative Gene Set Analysis

#' SEAparams S4 class implementation in R
#'
#' This S4 class contains the parameters to provide for SEA.
#'
#' @slot treat_lfc numeric, lfc parameter passed to
#' \code{treat} function (default: 0).
#' @slot de_cutoff numeric, cutoff value to define a gene as differentialy
#' expressed (default: 0.01).
#' @slot adjust_method character, method parameter passed to
#' \code{\link[stats]{p.adjust}} function (default: "fdr").
#' @slot de_genes (optional) character vector of differentialy expressed
#' genes,
#' if not provided it will be filled using the other parameters.
#' @slot br background reference to use, there are two possible options
#' for this slot (default: "briii"):
#' \itemize{
#' \item character indicating to use "bri" or "briii".
#' \item character vector indicating the genes to use as background
#' reference.
#' }
#' @slot test character indicating which test to use, it must be one of
#' "FisherTest", "HypergeoTest" or "BinomialTest" (default: "FisherTest").
#'
#' @docType methods
#' @name SEAparams-class
#' @rdname SEAparams-class
#' @seealso \code{GSEAparams-class}
#' @seealso \code{summary}
#'
#' @export SEAparams
#' @examples
#' ## Lets create the default SEAparams object.
#' mySeaParams <- SEAparams()
#' ## Lets create another SEAparams object with my default br genes. Make sure
#' ## these genes are present in the analyzed expression matrix rownames.
#' myBr <- as.character(1:10)
#' mySeaParamsOwnBr <- SEAparams(br = myBr)
#' ## Lets create another SEAparams object with my default differentialy
#' ## expressed genes. Make sure these genes are present in the analyzed
#' ## expression matrix rownames.
#' myDEGenes <- as.character(3:15)
#' mySeaParamsOwnDEG <- SEAparams(de_genes = myDEGenes)
#' ## Lets create another SEAparams object changing the differentialy
#' ## expressed genes parameters.
#' mySeaParamsOwnParams <- SEAparams(
#'   treat_lfc = 0.25, de_cutoff = 0.05,
#'   adjust_method = "none"
#' )
SEAparams <- setClass(
  Class = "SEAparams",
  slots = c(
    treat_lfc = "numeric",
    de_cutoff = "numeric",
    adjust_method = "character",
    de_genes = "character",
    br = "character",
    test = "character"
  ),
  prototype = list(
    treat_lfc = 0,
    de_cutoff = 0.01,
    adjust_method = "fdr",
    de_genes = as.character(NA),
    br = "briii",
    test = "FisherTest"
  ),
  validity = function(object) {
    treat_lfc_ok <- object@treat_lfc >= 0
    de_cutoff_ok <- object@de_cutoff >= 0 && object@de_cutoff <= 1
    adjust_method_ok <- object@adjust_method %in% p.adjust.methods
    br_ok <- object@br[[1]] %in% c("bri", "briii")

    # br must be bri, briii or a list of genes
    if (!br_ok) {
      br_ok <- length(unique(object@br)) > 0 &&
        any(!unique(object@br) == "")
    }

    # checking if test is valid
    test_ok <- length(object@test) == 1 &&
      object@test %in% c("FisherTest", "HypergeoTest", "BinomialTest")

    return(treat_lfc_ok && de_cutoff_ok && adjust_method_ok && br_ok &&
      test_ok)
  }
)

setClassUnion("SEAparamsOrNULL", c("SEAparams", "NULL"))