R/GSEAparams-class.R

In jcrodriguez1989/MIGSA: Massive and Integrative Gene Set Analysis

#' GSEAparams S4 class implementation in R
#'
#' This S4 class contains the parameters to provide for GSEA.
#'
#' @slot perm_number number of permutations for p-value calculation
#' (default: 200).
#' @slot min_sz minimum size of gene sets (number of genes in a gene set)
#' to be included in the analysis (default: 5).
#' @slot pv estimate of the variance associated with each observation
#' (default: 0).
#' @slot w1 weight 1, parameter used to calculate the prior variance
#' obtained with class size var.constant. This penalizes especially small
#' classes and small subsets. Values around 0.1 - 0.5 are expected to be
#' reasonable. (default: 0.2).
#' @slot w2 weight 2, parameter used to calculate the prior variance
#' obtained with the same class size as that of the analyzed class. This
#' penalizes small subsets from the gene list. Values around 0.3 and 0.5 are
#' expected to be reasonable (default: 0.5).
#' @slot vc size of the reference class used with wgt1. (default: 10).
#'
#' @docType methods
#' @name GSEAparams-class
#' @rdname GSEAparams-class
#' @seealso \code{\link{SEAparams-class}}
#' @seealso \code{\link{summary}}
#' @export GSEAparams
#' @examples
#' ## Lets create the default GSEAparams object.
#' myGseaParams <- GSEAparams()
#' ## Lets create another GSEAparams object with 500 permutations.
#' myGseaParams500Perms <- GSEAparams(perm_number = 500)
GSEAparams <- setClass(
  Class = "GSEAparams",
  slots = c(
    perm_number = "numeric",
    min_sz = "numeric",
    pv = "numeric",
    w1 = "numeric",
    w2 = "numeric",
    vc = "numeric"
  ),
  prototype = list(
    perm_number = 200,
    min_sz = 5,
    pv = 0,
    w1 = 0.2,
    w2 = 0.5,
    vc = 10
  ),
  validity = function(object) {
    perm_number_ok <- object@perm_number > 1
    min_sz_ok <- object@min_sz >= 0
    pv_ok <- object@pv >= 0
    w1_ok <- object@w1 >= 0
    w2_ok <- object@w2 >= 0
    vc_ok <- object@vc >= 0

    return(perm_number_ok && min_sz_ok && pv_ok && w1_ok && w2_ok &&
      vc_ok)
  }
)

setClassUnion("GSEAparamsOrNULL", c("GSEAparams", "NULL"))