R/SEAparams.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' @include SEAparams-class.R
setGeneric(name = "treat_lfc", def = function(object) {
  standardGeneric("treat_lfc")
})

setMethod(
  f = "treat_lfc", signature = "SEAparams",
  definition = function(object) {
    return(object@treat_lfc)
  }
)

setGeneric(name = "br", def = function(object) {
  standardGeneric("br")
})

setMethod(
  f = "br", signature = "SEAparams",
  definition = function(object) {
    return(object@br)
  }
)

setGeneric(name = "adjust_method", def = function(object) {
  standardGeneric("adjust_method")
})

setMethod(
  f = "adjust_method", signature = "SEAparams",
  definition = function(object) {
    return(object@adjust_method)
  }
)

setGeneric(name = "de_genes", def = function(object) {
  standardGeneric("de_genes")
})

setMethod(
  f = "de_genes", signature = "SEAparams",
  definition = function(object) {
    return(object@de_genes)
  }
)

setGeneric(name = "de_genes<-", def = function(object, value) {
  standardGeneric("de_genes<-")
})

setReplaceMethod(
  f = "de_genes", signature = "SEAparams",
  definition = function(object, value) {
    object@de_genes <- value
    validObject(object)
    return(object)
  }
)

setGeneric(name = "de_cutoff", def = function(object) {
  standardGeneric("de_cutoff")
})

setMethod(
  f = "de_cutoff", signature = "SEAparams",
  definition = function(object) {
    return(object@de_cutoff)
  }
)

setGeneric(name = "test", def = function(object) {
  standardGeneric("test")
})

setMethod(
  f = "test", signature = "SEAparams",
  definition = function(object) {
    return(object@test)
  }
)