R/accessors.R

In xpastor/CopyNeutralIMA: Copy Neutral Illumina Methylation Arrays

#' Accessor to the data objects.
#'
#' igetCopyNeutralRGSet simplifies the access to the data of the package in
#' ExperimentHub. The allowed values matched of those in the array definition of
#' the RGChannelSet objects from package 'minfi'.
#' If 'ima' is set to 'IlluminaHumanMethylation450k' it will return the object
#' with index 'EH1453' in ExperimentHub; if set to
#' 'IlluminaHumanMethylationEPIC' it will return the object with index 'EH1454'.
#'
#' @param ima a character string specifying for which array type to retrieve
#'   data. Valid values are 'IlluminaHumanMethylation450k' and 
#'   'IlluminaHumanMethylationEPIC'.
#'
#' @return A \code{\link[minfi]{RGChannelSet-class}} object
#'
#' @export
#' 
#' @import ExperimentHub
#'
#' @examples
#' rgset_450k <- getCopyNeutralRGSet('IlluminaHumanMethylation450k')
#' rgset_450k
getCopyNeutralRGSet <- function(ima=c('IlluminaHumanMethylation450k',
                                      'IlluminaHumanMethylationEPIC'))
{
    ima <- match.arg(ima)
    eh <- ExperimentHub()
    # load the reference dataset
    rgset <- loadResources(eh, package='CopyNeutralIMA', filterBy=ima)
    return(rgset[[1]])
}