R/app-edgerTwoGroups.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


ezMethodEdger <- function(input = NA, output = NA, param = NA) {
  require(withr)
  cwd <- getwd()
  setwdNew(basename(output$getColumn("Report")))
  defer(setwd(cwd))

  stopifnot(param$sampleGroup != param$refGroup)

  input <- cleanupTwoGroupsInput(input, param)
  param$groupingName <- param$grouping
  param$grouping <- input$getColumn(param$grouping)
  if (ezIsSpecified(param$grouping2) && length(param$grouping2) == 1) {
    param$grouping2Name <- param$grouping2
    param$grouping2 <- input$getColumn(param$grouping2)
    groupNum <- as.numeric(param$grouping2)
    if (all(!is.na(groupNum))){
      param$grouping2 <- setNames(groupNum, names(param$grouping2))
    }
  }

  rawData <- loadCountDataset(input, param)
  if (isError(rawData)) {
    writeErrorReport("00index.html", param = param, error = rawData$error)
    return("Error")
  }

  deResult <- twoGroupCountComparison(rawData)
  if (isError(deResult)) {
    writeErrorReport("00index.html", param = param, error = deResult$error)
    return("Error")
  }

  makeRmdReport(
    output = output, param = param, deResult = deResult,
    rmdFile = "twoGroups.Rmd", reportTitle = param$comparison
  )
  rmStatus <- file.remove(list.files(pattern="enrichr-.*rds"))
  return("Success")
}

##' @template app-template
##' @templateVar method ezMethodEdger(input=NA, output=NA, param=NA, htmlFile="00index.html")
##' @description Use this reference class to run a differential expression analysis with the application edgeR on two groups.
EzAppEdger <-
  setRefClass("EzAppEdger",
    contains = "EzApp",
    methods = list(
      initialize = function() {
        "Initializes the application using its specific defaults."
        runMethod <<- ezMethodEdger
        name <<- "EzAppEdger"
        appDefaults <<- rbind(
          testMethod = ezFrame(
            Type = "character", DefaultValue = "glm",
            Description = "which test method in edgeR to use: glm or exactTest"
          ),
          normMethod = ezFrame(
            Type = "character", DefaultValue = "TMM",
            Description = "edgeR's norm method: TMM, upperquartile, RLE, or none"
          ),
          useRefGroupAsBaseline = ezFrame(
            Type = "logical", DefaultValue = FALSE,
            Description = "should the log-ratios be centered at the reference samples"
          ),
          onlyCompGroupsHeatmap = ezFrame(
            Type = "logical", DefaultValue = FALSE,
            Description = "Only show the samples from comparison groups in heatmap"
          ),
          priorCount = ezFrame(
            Type = "numeric", DefaultValue = 10,
            Description = "prior count to be added to shrink the log-fold-changes"
          ),
          deTest = ezFrame(
            Type = "character", DefaultValue = "QL",
            Description = "edgeR's differential expression test method: QL or LR"
          ),
          runGfold = ezFrame(
            Type = "logical", DefaultValue = FALSE,
            Description = "should gfold run"
          ),
          doPrecomputeEnrichr = ezFrame(
            Type = "logical", DefaultValue = FALSE,
            Description = "should enrichr be precomputed"
          )
        )
      }
    )
  )