R/IGSAinput-getterSetters.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' Accessors for IGSAinput class
#'
#' Getters and setters functions to access IGSAinput object slots.
#'
#' @param object IGSAinput object.
#' @param value value to replace in the slot.
#'
#' @return Modified IGSAinput object or desired slot.
#'
#' @docType methods
#' @name IGSAinput-getterSetters
#' @rdname IGSAinput-getterSetters
#' @seealso \code{\link{IGSAinput-class}}
#' @include IGSAinput-class.R
#'
#' @examples
#' ## Lets create a basic IGSAinput object.
#' ## First create a expression matrix.
#' maData <- matrix(rnorm(10000), ncol = 4)
#' rownames(maData) <- 1:nrow(maData)
#' # It must have rownames (gene names).
#' maExprData <- new("MAList", list(M = maData))
#' ## Now lets create the FitOptions object.
#' myFOpts <- FitOptions(c("Cond1", "Cond1", "Cond2", "Cond2"))
#' ## And now we can create our IGSAinput ready for MIGSA.
#' igsaInput <- IGSAinput(
#'   name = "igsaInput", expr_data = maExprData,
#'   fit_options = myFOpts
#' )
#' ## Lets get igsaInput values, and modify its name.
#' name(igsaInput)
#' name(igsaInput) <- "newName"
#' fitOptions(igsaInput)
#' exprData(igsaInput)
#' geneSetsList(igsaInput)
#' gseaParams(igsaInput)
#' seaParams(igsaInput)
setGeneric(name = "IGSAinput-getterSetters", def = function(object) {
  standardGeneric("IGSAinput-getterSetters")
})

#' @name name
#' @rdname IGSAinput-getterSetters
#' @aliases name,IGSAinput-method
#' @exportMethod name
#'
setGeneric(name = "name", def = function(object) {
  standardGeneric("name")
})

#' @rdname IGSAinput-getterSetters
#' @aliases name,IGSAinput-method
#'
setMethod(
  f = "name", signature = "IGSAinput",
  definition = function(object) {
    return(object@name)
  }
)

#' @name name<-
#' @rdname IGSAinput-getterSetters
#' @aliases name<-,IGSAinput-method
#' @exportMethod name<-
#'
setGeneric(name = "name<-", def = function(object, value) {
  standardGeneric("name<-")
})

#' @rdname IGSAinput-getterSetters
#' @aliases name<-,IGSAinput-method
#'
setReplaceMethod(
  f = "name", signature = "IGSAinput",
  definition = function(object, value) {
    object@name <- value
    validObject(object)
    return(object)
  }
)

#' @name fitOptions
#' @rdname IGSAinput-getterSetters
#' @aliases fitOptions,IGSAinput-method
#' @exportMethod fitOptions
#'
setGeneric(name = "fitOptions", def = function(object) {
  standardGeneric("fitOptions")
})

#' @rdname IGSAinput-getterSetters
#' @aliases fitOptions,IGSAinput-method
#'
setMethod(
  f = "fitOptions", signature = "IGSAinput",
  definition = function(object) {
    return(object@fit_options)
  }
)

#' @name fitOptions<-
#' @rdname IGSAinput-getterSetters
#' @aliases fitOptions<-,IGSAinput-method
#' @exportMethod fitOptions<-
#'
setGeneric(name = "fitOptions<-", def = function(object, value) {
  standardGeneric("fitOptions<-")
})

#' @rdname IGSAinput-getterSetters
#' @aliases fitOptions<-,IGSAinput-method
#'
setReplaceMethod(
  f = "fitOptions", signature = "IGSAinput",
  definition = function(object, value) {
    object@fit_options <- value
    validObject(object)
    return(object)
  }
)

#' @name exprData
#' @rdname IGSAinput-getterSetters
#' @aliases exprData,IGSAinput-method
#' @exportMethod exprData
#'
setGeneric(name = "exprData", def = function(object) {
  standardGeneric("exprData")
})

#' @rdname IGSAinput-getterSetters
#' @aliases exprData,IGSAinput-method
#'
setMethod(
  f = "exprData", signature = "IGSAinput",
  definition = function(object) {
    return(object@expr_data)
  }
)

#' @name exprData<-
#' @rdname IGSAinput-getterSetters
#' @aliases exprData<-,IGSAinput-method
#' @exportMethod exprData<-
#'
setGeneric(name = "exprData<-", def = function(object, value) {
  standardGeneric("exprData<-")
})

#' @rdname IGSAinput-getterSetters
#' @aliases exprData<-,IGSAinput-method
#'
setReplaceMethod(
  f = "exprData", signature = "IGSAinput",
  definition = function(object, value) {
    object@expr_data <- value
    validObject(object)
    return(object)
  }
)

#' @name geneSetsList
#' @rdname IGSAinput-getterSetters
#' @aliases geneSetsList,IGSAinput-method
#' @exportMethod geneSetsList
#'
setGeneric(name = "geneSetsList", def = function(object) {
  standardGeneric("geneSetsList")
})

#' @rdname IGSAinput-getterSetters
#' @aliases geneSetsList,IGSAinput-method
#'
setMethod(
  f = "geneSetsList", signature = "IGSAinput",
  definition = function(object) {
    return(object@gene_sets_list)
  }
)

#' @name geneSetsList<-
#' @rdname IGSAinput-getterSetters
#' @aliases geneSetsList<-,IGSAinput-method
#' @exportMethod geneSetsList<-
#'
setGeneric(name = "geneSetsList<-", def = function(object, value) {
  standardGeneric("geneSetsList<-")
})

#' @rdname IGSAinput-getterSetters
#' @aliases geneSetsList<-,IGSAinput-method
#'
setReplaceMethod(
  f = "geneSetsList", signature = "IGSAinput",
  definition = function(object, value) {
    object@gene_sets_list <- value
    validObject(object)
    return(object)
  }
)

#' @name gseaParams
#' @rdname IGSAinput-getterSetters
#' @aliases gseaParams,IGSAinput-method
#' @exportMethod gseaParams
#'
setGeneric(name = "gseaParams", def = function(object) {
  standardGeneric("gseaParams")
})

#' @rdname IGSAinput-getterSetters
#' @aliases gseaParams,IGSAinput-method
#'
setMethod(
  f = "gseaParams", signature = "IGSAinput",
  definition = function(object) {
    return(object@gsea_params)
  }
)

#' @name gseaParams<-
#' @rdname IGSAinput-getterSetters
#' @aliases gseaParams<-,IGSAinput-method
#' @exportMethod gseaParams<-
#'
setGeneric(name = "gseaParams<-", def = function(object, value) {
  standardGeneric("gseaParams<-")
})

#' @rdname IGSAinput-getterSetters
#' @aliases gseaParams<-,IGSAinput-method
#'
setReplaceMethod(
  f = "gseaParams", signature = "IGSAinput",
  definition = function(object, value) {
    object@gsea_params <- value
    validObject(object)
    return(object)
  }
)

#' @name seaParams
#' @rdname IGSAinput-getterSetters
#' @aliases seaParams,IGSAinput-method
#' @exportMethod seaParams
#'
setGeneric(name = "seaParams", def = function(object) {
  standardGeneric("seaParams")
})

#' @rdname IGSAinput-getterSetters
#' @aliases seaParams,IGSAinput-method
#'
setMethod(
  f = "seaParams", signature = "IGSAinput",
  definition = function(object) {
    return(object@sea_params)
  }
)

#' @name seaParams<-
#' @rdname IGSAinput-getterSetters
#' @aliases seaParams<-,IGSAinput-method
#' @exportMethod seaParams<-
#'
setGeneric(name = "seaParams<-", def = function(object, value) {
  standardGeneric("seaParams<-")
})

#' @rdname IGSAinput-getterSetters
#' @aliases seaParams<-,IGSAinput-method
#'
setReplaceMethod(
  f = "seaParams", signature = "IGSAinput",
  definition = function(object, value) {
    object@sea_params <- value
    validObject(object)
    return(object)
  }
)