R/app-countQC.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

###################################################################
# Functional Genomics Center Zurich
# This code is distributed under the terms of the GNU General
# Public License Version 3, June 2007.
# The terms are available here: http://www.gnu.org/licenses/gpl.html
# www.fgcz.ch


ezMethodCountQC = function(input=NA, output=NA, param=NA,
                           htmlFile="00index.html"){
  setwdNew(basename(output$getColumn("Report")))
  dataset <- input$meta
  if (param$useFactorsAsSampleName){
    dataset$Name = rownames(dataset)
    rownames(dataset) = addReplicate(apply(ezDesignFromDataset(dataset), 1, 
                                           paste, collapse="_"))
  }
  input$meta <- dataset
  rawData <- loadCountDataset(input, param)
  
  if (isError(rawData)){
    writeErrorReport(htmlFile, param=param, error=rawData$error)
    return("Error")
  }
  
  metadata(rawData)$output <- output
  makeRmdReport(rawData=rawData, rmdFile="CountQC.Rmd", 
                reportTitle="CountQC", selfContained = TRUE)
  
  return("Success")
}

##' @template app-template
##' @templateVar method ezMethodCountQC(input=NA, output=NA, param=NA, htmlFile="00index.html")
##' @description Use this reference class to run 
EzAppCountQC <-
  setRefClass("EzAppCountQC",
              contains = "EzApp",
              methods = list(
                initialize = function()
                {
                  "Initializes the application using its specific defaults."
                  runMethod <<- ezMethodCountQC
                  name <<- "EzAppCountQC"
                  appDefaults <<- rbind(runGO=ezFrame(Type="logical", DefaultValue=TRUE, Description="whether to run the GO analysis"),
                                        nSampleClusters=ezFrame(Type="numeric", DefaultValue=6, Description="Number of SampleClusters, max value 6"))
                }
              )
  )