R/orphanMethods.R

In RamsinghLab/ozymandias: Tools for region- and process-centric analyses of multiple assay types

## ease transition from SummarizedExperiment to RangedSummarizedExperiment
setMethod("update", signature(object = "GenomicRatioSet"),
  function(object) {
      getOldAssay <- function(x, y) slot(x, "assays")[["data"]][[y]]
      grset <- GenomicRatioSet(gr=slot(object, "rowData"),
                               Beta=getOldAssay(object, "Beta"),
                               M=getOldAssay(object, "M"),
                               CN=getOldAssay(object, "CN"),
                               pData=slot(object, "colData"),
                               annotation=slot(object, "annotation"),
                               preprocessMethod=slot(object,"preprocessMethod"))
      metadata(grset) <- as(slot(object, "exptData"), "list")
      return(grset)
  })