require("minfi", quietly = TRUE)
require("BiocGenerics", quietly = TRUE)
require("data.table", quietly = TRUE)
require("GEOquery", quietly = TRUE)
require("rtracklayer", quietly = TRUE)
require("FDb.InfiniumMethylation.hg19", quietly = TRUE)

args <- commandArgs(trailingOnly = TRUE)
GSE = args[1] 
output = args[2] 

getAnnotationString <- function(annotation) {
  if(length(annotation) == 1)
    return(sprintf("%sanno", annotation))
  if(all(c("array", "annotation") %in% names(annotation)))
    return(sprintf("%sanno.%s", annotation["array"], annotation["annotation"]))
  stop("unable to get the annotation string for this object")
}

default.450k.annotation <- "ilmn12.hg19"



function (GSE = GSE, array = "IlluminaHumanMethylation450k", annotation = default.450k.annotation,
          what = c("Beta", "M"), mergeManifest = FALSE, i = 1){
  
  
  gset <- getGEO(GSE)
  gset <- gset[[1]]
  
  platform <- annotation(gset)
  
  ann <- getAnnotationString(c(array = array, annotation = annotation))
  if (!require(ann, character.only = TRUE)) 
    stop(sprintf("cannot load annotation package %s", ann))
  
  object <- get(ann)
  
  gr <- getLocations(object, mergeManifest = mergeManifest, 
                     orderByLocation = TRUE)
  locusNames <- names(gr)
  sampleNames(gset) <- gset$title
  common <- intersect(locusNames, fData(gset)$Name)
  if (length(common) == 0) {
    stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
    ind1 <- match(common, fData(gset)$Name)
    ind2 <- match(common, locusNames)
    preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
    if (what == "Beta") {
      out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1, 
                                                                 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset), 
                             annotation = c(array = array, annotation = annotation), 
                             preprocessMethod = preprocessing)
    }
    else {
      out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL, 
                             M = exprs(gset)[ind1, , drop = FALSE], CN = NULL, 
                             pData = pData(gset), annotation = c(array = array, 
                                                                 annotation = annotation), preprocessMethod = preprocessing)
    }
    return(out)
  }
  save(out,file = output)
}