R/easyRNASeq-AnnotParam-accessors.R

In easyRNASeq: Count summarization and normalization for RNA-Seq data

#' Accessors for AnnotParam class
#'
#' These functions and generics define `accessors` (to get and set values) for
#' \code{\linkS4class{AnnotParam}} objects within the \pkg{easyRNASeq} package.
#' Implemented are:
#' \itemize{
#' \item datasource
#' \item type
#' }
#'
#' @aliases AnnotParam-accessors datasource
#' datasource,AnnotParam-method type,AnnotParam-method
#' @name easyRNASeq AnnotParam accessors
#' @rdname easyRNASeq-AnnotParam-accessors
#' @param x An object derived from class \code{AnnotParam}.
#' @param object An object derived from class \code{AnnotParam}.
#' @usage datasource(object)
#' \S4method{type}{AnnotParam}(x)
#' @return
#' The value of the corresponding slot.
#' @author Nicolas Delhomme
#' @keywords manip
#' @seealso The \code{\link[easyRNASeq:easyRNASeq-AnnotParam-class]{AnnotParam}} class.
#' The type and organism generics are imported from the \code{\link[BSgenome:BSgenome-class]{BSgenome}} and
#' \code{\link[Biostrings:XString-class]{Biostrings}} package, respectively.
#' @examples
#' # fetch the example data
#' Dm.annot <- fetchData("Dmel-mRNA-exon-r5.52.gff3.gz")
#'
#' annot <- AnnotParam(datasource=Dm.annot)
#' # get the datasource Parameter
#' datasource(annot)
#'

setMethod(f="datasource",
          signature="AnnotParam",
          definition=function(object){
            object@datasource
          })

setMethod(f="type",
          signature="AnnotParam",
          definition=function(x){
            switch(class(x),
                   "AnnotParamCharacter"=x@type,
                   NULL)
          })