R/AromaPipeline.R

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

# @author "HB"
setConstructorS3("AromaPipeline", function(dataSet=NULL, ..., .class=NULL) {
  # Argument 'dataSet':
  if (!is.null(dataSet)) {
    if (!is.null(.class)) {
      dataSet <- Arguments$getInstanceOf(dataSet, .class)
    }
  }

  extend(Object(), "AromaPipeline",
    .dataSet = dataSet,
    .result = NULL
  )
})


setMethodS3("getSteps", "AromaPipeline", abstract=TRUE)

setMethodS3("nbrOfSteps", "AromaPipeline", function(this, ...) {
  steps <- getSteps(this)
  length(steps)
})


setMethodS3("process", "AromaPipeline", function(this, ..., verbose=FALSE) {
  assertAnnotationData(this)

  ds <- getInputDataSet(this)
  steps <- getSteps(this)
  for (kk in seq_along(steps)) {
    step <- steps[[kk]]
    ds <- step(ds, verbose=verbose)
  }

  this$.result <- ds

  ds
})