R/classes.R

In haowulab/SC2P: Two phase differential expression for single-cell RNA-seq

##################################################################
## Define sc2pSet class mimicing ExpressionSet class from Biobase
##################################################################

setClass("sc2pSet", contains="eSet",
         prototype = prototype(
         new("VersionedBiobase",
             versions=c(classVersion("eSet"), sc2pSet="1.0.0"))))


setMethod("initialize", "sc2pSet",
          function(.Object,
                   assayData = assayDataNew(exprs=exprs, Z=Z, Offset=Offset),
                   exprs=new("matrix"),
                   Z=new("matrix"),
                   Offset=new("matrix"),
                   ...){
              if (!missing(assayData) && !missing(Z) && dim(assayData) != dim(Z)){
                  stop("Z is not in the same dimensions as assayData")
              }
              callNextMethod(.Object, assayData=assayData, ...)
          })

setValidity("sc2pSet", function(object){
    assayDataValidMembers(assayData(object), c("Z", "Offset"))
})