R/AllClasses.R

In roar: Identify differential APA usage from RNA-seq alignments

# This class will hold a GenomicAnnotation (pre-post GTF) and count results in a RangedSummarizedExperiment
setClass("RoarDataset",
          contains = "RangedSummarizedExperiment", # Superclasses
          representation = representation( # Slots
             treatmentBams = "list",  #list of GAlignments 
             controlBams = "list",
             prePostCoords = "GRanges",
             postCoords = "GRanges",
             countsTreatment = "RangedSummarizedExperiment",
             countsControl = "RangedSummarizedExperiment",
             pVals = "RangedSummarizedExperiment",
             step = "numeric",
             paired = "logical",
             cores = "numeric"
          )
)
#validity=function(roc) length(roc@sens)==length(roc@mspec)
#          && length(roc@sens)==length(roc@test)
# check validity of kind of alignments, existence of PRE/POST ids -> moved in other methods.
# prototype -> default values

setClass("RoarDatasetMultipleAPA",
         representation = representation( # Slots
            treatmentBams = "list",  #list of GAlignments 
            controlBams = "list",
            geneCoords = "GRangesList",
            apaCoords = "GRangesList",
            fragments = "GRangesList",
            prePostDef = "list",
            roars = "list",
            step = "numeric",
            paired = "logical",
            corrTreatment = "numeric",
            corrControl = "numeric",
            cores = "numeric"
         ),
         prototype = list(
            geneCoords = GRangesList(),
            apaCoords = GRangesList(),
            fragments = GRangesList()
         )
)

setClass("ApaFragmentPrePost",
         representation = representation (
            name = "character",
            PREstart = "numeric",
            PREend = "numeric"
         )
)