--- a
+++ b/R/cleanMetadata.GSE34171.R
@@ -0,0 +1,130 @@
+#' @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")]
+