R/doGeneAnnotation.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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#'doGeneAnnotation
#'
#' Function that annotates a data set.
#'
#' @param AnotList List object that contains the parameters needed to carry out the analysis.
#' @export
#' @examples
#' \dontrun{
#' organisme <- "hsa"
#' AnotList <- list(fitMain = NULL, fitFileName = fitFileName, my.IDs = "entrezTable",
#'                  anotPackage = "org.Hs.eg", toHTML = TRUE, outputDir = outputDir,
#'                  anotFilename = "Annotations",
#'                  titleAnotations = "Annotations for all genes analyzed", specie = "homo sapiens",
#'                  info2show = c("Affymetrix", "EntrezGene", "GeneSymbol",
#'                                "GeneName", "KEGG", "GO"),
#'                  linksFile = linksFile, numGenesPerPage = NULL)
#'
#' BasicP::doGeneAnnotation(AnotList)}

doGeneAnnotation <- function(AnotList) {
  p <- AnotList

  if(!is.null(p$my.IDs)) EntrezIDs <-  eval(parse(text = p$my.IDs))

  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'")
    }
  }

  genes2annotate <- EntrezIDs[unique(rownames(fitMain$p.value))]

  genesAnnotated <- GeneAnnotation(egIDs = genes2annotate,
                                   anotPackage = orgPackage,
                                   toHTML = p$toHTML,
                                   outputDir = p$outputDir,
                                   filename = p$anotFilename,
                                   myTitle = p$titleAnotations,
                                   specie = organisme,
                                   info2show = p$info2show,
                                   linksFile = p$linksFile,
                                   maxGenes = p$numGenesPerPage)
  return(genesAnnotated)
}