R/AllClasses.R

In BiSeq: Processing and analyzing bisulfite sequencing data

setClass("BSrel",
         contains = "RangedSummarizedExperiment"
         )

setClass("BSraw",
         contains = "RangedSummarizedExperiment"
         )


setValidity("BSrel", function(object){
  if(length(assays(object)) != 1)
    return("The assays slot in BSrel object must be of length one.")
  if(!is(assay(object), "matrix"))
    return("The methLevel slot of an BSrel object must be a matrix.")
  if(mode(assay(object)) != "numeric")
    return("The methLevel matrix of an BSrel object must contain numeric data.")
}
            )

setValidity("BSraw", function(object){
  if(length(assays(object)) != 2)
    return("The assays slot in BSraw object must be of length two.")
  if(!(all( is.element(names(assays(object)), c("totalReads", "methReads")) )))
    return("The assays slot in BSraw object must contain totalReads and methReads.")
  if(!all( sapply(assays(object), is.matrix) ))
    return("The totalReads and methReads slots of an BSraw object must be matrices.")
  if(!all(sapply(assays(object), typeof) == "integer" ))
    return("The totalReads and methReads matrices of an BSraw object must contain integer data.")
}
            )