R/doMultCompAnalysis.R

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

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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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#' doMultCompAnalysis
#'
#' Function for make the comparative analysis.
#' @param mcPar List object that contains the parameters.
#' @examples
#' \dontrun{
#' mcParsList <- list()
#' compName <- c("Group1", "Group2")
#' wCont <- 1:ncol(cont.matrix)
#' pValCutOff <- c(0.01, 0.01)
#' adjMethod <- c("none", "none")
#' minLogFoldChange <- c(1, 1)
#' for(i in 1:length(compName))
#' {
#'   pvalType <- ifelse(adjMethod[i] == "none", "p-values", "adj. p-values")
#'   mci <- list(fitMain = fitMain,
#'               fitFileName = fitFileName,
#'               whichContrasts = wCont[[i]],
#'               comparisonName = compName[i],
#'               titleText = paste("for", pvalType, "<", pValCutOff[i],
#'                                 "and |logFC| >", minLogFoldChange[i]),
#'               anotPackage = "org.Hs.eg",
#'               my.symbols = symbolsTable,
#'               outputDir = outputDir,
#'               fileOfLinks = linksFile,
#'               multCompMethod = "separate",
#'               adjustMethod = adjMethod[i],
#'               selectionType = "any",
#'               P.Value.cutoff = pValCutOff[i],
#'               plotVenn = TRUE,
#'               colsVenn = NULL,
#'               vennColors= c("red", "yellow", "green", "blue", "pink"),
#'               cexVenn = 1,
#'               geneListFName = paste("geneList", compName[i], pvalType,
#'                                     "LT", pValCutOff[i], "Rda", sep = "."),
#'               minLogFC = minLogFoldChange[i],
#'               csvType = csvType)
#'
#'   mcParsList <- add2parsList(mcParsList, mci)
#' }
#'
#' for(ix in 1:length(mcParsList))
#' {
#'   geneList.MCi <- BasicP::doMultCompAnalysis(mcParsList[ix])
#' }
#' }
#' @export

doMultCompAnalysis <- function(mcPar) {
  p <- mcPar[[1]]

  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 dona error!!!
    } else {
      stop("Error, Cal subministrar un nom d'arxiu o d'objecte 'fitMain'")
    }
  }

  geneList <-  multipleComp(fitMain = fitMain,
                            whichContrasts = p$whichContrasts,
                            comparisonName = p$comparisonName,
                            titleText = p$titleText,
                            outputDir = p$outputDir,
                            anotPackage = p$anotPackage,
                            my.symbols = symbolsTable,
                            linksFile = p$fileOfLinks,
                            multCompMethod = p$multCompMethod,
                            adjustMethod = p$adjustMethod,
                            selectionType = p$selectionType,
                            P.Value.cutoff = p$P.Value.cutoff,
                            plotVenn = p$plotVenn,
                            colsVenn = p$colsVenn,
                            vennColors = p$vennColors,
                            cexVenn = p$cexVenn,
                            geneListFName = p$geneListFName,
                            csvType = p$csvType,
                            minLFC = p$minLogFC)

  return (geneList)
}