#' @rdname cleanMetadata

#' @details

#'    GSE34171:\cr

#'    The cleanup of GSE34171 (MDFCI) adds three batches corresponding to each

#'    platform (HG-U133 plus 2, HG-U133A, HG-U133B).

#' @export

cleanMetadata.GSE34171 <- function(meta_data) {

  message("Cleaning GSE34171 (MDFCI)!")

  # Generic clean

  suppressMessages(meta_data <- cleanMetadata.data.frame(meta_data))

  # Added factor describing the batches and CEL files

  meta_data$Batch <- factor(meta_data$platform_id,

                            levels = c("GPL570", "GPL96", "GPL97"))

  meta_data$CEL <-

   gsub("^.+/(GSM[0-9]+)\\..+$", "\\1", meta_data$supplementary_file)

  meta_data$GSM <- as.character(meta_data$geo_accession)

  rownames(meta_data) <- meta_data$CEL

  return(meta_data)

}

#   meta_data_Clinical <-

#     read.table(file=file.path(MDFCI.ext.dir, "../RawData", "Metadata",

#                               "GSE34171_clinical_info.txt"),

#                header = TRUE, stringsAsFactors = FALSE)

#

#   meta_data_Outcome <-

#     read.table(file=file.path(MDFCI.ext.dir, "../RawData", "Metadata",

#                               "GSE34171_outcome_data.txt"),

#                skip = 2, stringsAsFactors = FALSE)

#   colnames(meta_data_Outcome) <- c("Title", "Class", "os", "Followup")

#

#   meta_data_Sample <-

#     read.csv(file=file.path(MDFCI.ext.dir, "../RawData", "Metadata",

#                             "sample.csv"),

#              stringsAsFactors = FALSE)

#

#   meta_data <- merge(merge(meta_data_Sample,

#                                meta_data_Outcome, all.x=TRUE, all.y=TRUE),

#                          meta_data_Clinical, all.x=TRUE)

#

#   table(meta_data$Title, meta_data$Platform)

#

#   xx <- meta_data_Sample[meta_data_Sample$Title %in% meta_data$Title &

#                                meta_data_Sample$Platform == "GPL570" , c(1, 2)]

#

#   colnames(xx)[1] <- "HGU133Plus2"

#   meta_data <- merge(meta_data, xx, all.x = TRUE)

#

#   xx <- meta_data_Sample[meta_data_Sample$Title %in% meta_data$Title &

#                                meta_data_Sample$Platform == "GPL6801" , c(1, 2)]

#

#   colnames(xx)[1] <- "GenomeWideSNP6"

#   meta_data <- merge(meta_data, xx, all.x = TRUE)

#

#

#   xx <- meta_data_Sample[meta_data_Sample$Title %in% meta_data$Title &

#                                meta_data_Sample$Platform == "GPL96" , c(1, 2)]

#

#   colnames(xx)[1] <- "HGU133A"

#   meta_data <- merge(meta_data, xx, all.x = TRUE)

#

#   xx <- meta_data_Sample[meta_data_Sample$Title %in% meta_data$Title &

#                                meta_data_Sample$Platform == "GPL97" , c(1, 2)]

#

#   colnames(xx)[1] <- "HGU133B"

#   meta_data <- merge(meta_data, xx, all.x = TRUE)

#

#

#

#

#   meta_data <- meta_data[!duplicated(meta_data$Title),]

#

#   meta_data$IPI <- as.factor(as.numeric(meta_data$IPI))

#

#   meta_data$ipi.hl <- ifelse(is.na(meta_data$IPI), NA, "0-1")

#   meta_data$ipi.hl[meta_data$IPI %in% c(2, 3)] <- "2-3"

#   meta_data$ipi.hl[meta_data$IPI %in% c(4, 5)] <- "4-5"

#

#   table(meta_data[, c("IPI", "ipi.hl")])

#

#   Monti.Suppl5 <-

#     read.delim("../Litterature/Monti_Suppl5_NIHMS398769-supplement-06(1).txt",

#                stringsAsFactors = FALSE)

#

#   rownames(Monti.Suppl5) <- Monti.Suppl5$CaseID

#

#   colnames(Monti.Suppl5)[5] <- "WrightClass"

#

#

#

#   meta_data <- merge(meta_data, Monti.Suppl5,

#                          by.x = "Title", all.x=TRUE,

#                          by.y = "CaseID")

#

#

#   meta_data$TP53.mut[meta_data$TP53.mut == "na"] <- NA

#

#

#

#

#

#   ABCGCBclass <- read.delim(file.path(MDFCI.ext.dir,

#                                       "../ABCGCBclassification",

#                                       "ABCGCBclass.txt"))

#   meta_data$WrightClass_own <-

#     ABCGCBclass[meta_data$Title,2]

#

#   ABCGCBclass[paste(meta_data$GPL570, ".CEL", sep = ""),2]

#

#

#   meta_data$OS <- Surv(meta_data$os/365.25, meta_data$Followup)

#

#   os5  <- ifelse(meta_data$os/365.25 > 5, 5, meta_data$os/365.25)

#   ios5 <- pmin(ifelse(meta_data$os/365.25 > 5, 0, 1), meta_data$Followup)

#

#   meta_data$OS5 <- Surv(as.numeric(os5), ios5)

#

#

#   meta_data$HGU133Plus2[meta_data$HGU133Plus2 == "GSM844275"] <- NA

#

#   meta_data <- meta_data[, c(

#     "Title", "Class", "os", "Followup", "Type", "Entity", "Primary",

#     "IPI", "HGU133Plus2", "GenomeWideSNP6", "HGU133A", "HGU133B", "ipi.hl",

#     "SNP.ScanID", "GEP.SampleID", "CCC..Best.10.13.", "WrightClass",

#     "WrightClass_own", "TP53.mut")]