R/doGOAnalysis.R

In uebvhir/BasicP4microArrays: Functions to create and run simple-to-complex microarray analysis pipeline

############################################################

loadFromFile <- function(fileName, pos = 1) {
  tempEnv <- new("environment")
  load(fileName, tempEnv)
  varNames <-ls(tempEnv)
  myVarName <- varNames[pos]
  load(fileName)
  myVar <- eval(parse(text = myVarName))
  return(myVar)
}
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extractSinonims <- function(my.strings) {
  my.sinonims <- list()
  if(runMulticore == 1 || runMulticore == 3) {
    my.sinonims <- mclapply(my.strings, function(x) unlist(strsplit(x, " /// ")))
  } else {
    my.sinonims <- lapply(my.strings, function(x) unlist(strsplit(x, " /// ")))
  }

  return(my.sinonims)
}
###################################################
midSinonims <- function(my.IDs) {
  my.indexes <- grep(" /// ", my.IDs)
  my.sinonimIDs <- my.IDs[my.indexes]
  my.IDs[my.indexes] <- extractSinonims(my.sinonimIDs)
  return(my.IDs)
}

###################################################

#'doGOAnalysis
#'
#'Function to interate with GOAnalysis
#'
#'@param GOPar List object that contains the parameters needed to carry out the analysis.
#'@return GOResult
#'@examples
#' \dontrun{
#' GOResult<-BasicP::GOAnalysis(fitMain = fitMain, whichContrasts = wCont,
#'                              comparison.Name = "Estudi", outputDir = outputDir,
#'                              anotPackage = "org.Hs.eg", my.IDs = entrezTable,
#'                              addGeneNames = TRUE, fileOfLinks = linksFile, thrLogFC = 1,
#'                              cutoffMethod = "adjusted",
#'                              P.Value.cutoff = rep(0.05, length(wCont)), pval = 0.01,
#'                              min.count = 3, ontologias = c("MF", "BP", "CC"),
#'                              testDirections = c("over", "under"), minNumGens = 0)
#'}
#'@export

doGOAnalysis <- function(GOPar) {
  p <- GOPar[[1]]

  if(!is.null(p$my.IDs)) EntrezIDs <-  eval(parse(text = p$my.IDs)) #  Si se hace el eval solo guarda el ultimo id

  if(!is.null(p$fitFileName)) {
    fitMain <- loadFromFile(file.path(p$outputDir, p$fitFileName))
  } else {
    if(!is.null(p$fitMain)) {
      fitMain <- eval(parse(text = p$fitMain)) # Posar-hi un tryCatch per poder sortir si d??na error!!!
    } else {
      stop("Error, Cal subministrar un nom d'arxiu o d'objecte 'fitMain'")
    }
  }

  if(!is.null(p$my.IDs)) my.IDs <- midSinonims(p$my.IDs)

  GOResult <- GOAnalysis(fitMain = fitMain,
                         whichContrasts = p$whichContrasts,
                         comparison.Name = p$comparisonName,
                         outputDir = p$outputDir,
                         anotPackage = orgPackage,
                         my.IDs = EntrezIDs,
                         addGeneNames = p$addGeneNames,
                         fileOfLinks = p$fileOfLinks,
                         thrLogFC = p$minLogFC,
                         cutoffMethod = p$cutoffMethod,
                         P.Value.cutoff = p$P.Value.cutoff,
                         pval = p$pvalGOterms,
                         min.count = p$min.count,
                         ontologias = p$ontologias,
                         testDirections = p$testDirections,
                         minNumGens = p$minNumGens)

  return(GOResult)
}