Xavi

###################################################
### chunk number 3: annotations
###################################################
stopifnot(require(Biobase, lib.loc = mylib))

source(file.path(codeDir,"AnalysisFunctions2Pack.R"))

arrayType <- "{$f_179}"

chipPackAvailable <- "{$f_20}"       # Si existeix un paquet BioC pel xip es posa a TRUE
if (chipPackAvailable){
  anotPackage <- "{$f_21}"             # Pot ser per exemple 'hgu133plus2' o 'mouse4302'
  anotations.FileName <- "{$f_22}"   # Si hi ha chipPackage ha de ser NULL
  symbolsTable <- "{$f_23}"          # Si hi ha chipPackage ha de ser NULL
  entrezTable <- "{$f_24}"           # Si hi ha chipPackage ha de ser NULL
}else{
                               ### Si no hi ha paquet BioC pel xip
  anotPackage <- "{$f_21}"            # Un paquet d'organisme com 'org.Hs.eg' o 'org.Mm.eg'
  anotations.FileName <- "{$f_22}"    # Un paquet d'anotacions fet a ma 'HEAnnotation.txt'
  if (!is.null(anotations.FileName)) {
    if (!(exists("symbolsTable")))
      symbolsTable <- creaAnot(dataDir, anotations.FileName, "Gene.Symbol")
    if (!(exists("entrezTable")))
      entrezTable <- creaAnot(dataDir,  anotations.FileName, "Entrez.Gene.ID")
    my.annotations<-cbind(Entrez=entrezTable, Symbols=symbolsTable)
    write.table(my.annotations, file=file.path(dataDir, "my.annotations.txt"), sep="\t", quote=F)
  }
}