--- a
+++ b/R/cleanMetadata.GSE10846.R
@@ -0,0 +1,146 @@
+#' @rdname cleanMetadata
+#' @details
+#'    GSE10846:\cr
+#'    The cleanup of GSE10846 (LLMPP) adds two batches corresponding to each
+#'    the CHOP and the R-CHOP cohort.
+#' @export
+cleanMetadata.GSE10846 <- function(meta_data) {
+  message("Cleaning GSE10846 (LLMPP)!")
+
+  # Generic clean
+  suppressMessages(meta_data <- cleanMetadata.data.frame(meta_data))
+
+  stopifnot(requireNamespace("survival"))
+
+  # Helper functions
+  wo.na <- function(x) sum(x[!is.na(x)])
+  n.is.na <- function(x) sum(is.na(x))
+  IPI <- function(age, ECOG, stage, No.Extra.Nodal, LDH) {
+    a <- ifelse(age            >  60, 1, 0)
+    b <- ifelse(ECOG           >   1, 1, 0)
+    c <- ifelse(No.Extra.Nodal >=  2, 1, 0)
+    d <- ifelse(stage          >   2, 1, 0)
+    e <- ifelse(LDH            >   1, 1, 0)
+
+    ipi <- data.frame(a = a, b = b, c = c, d = d, e = e)
+    score  <- apply(ipi, 1, sum)
+    score2 <- apply(ipi, 1, wo.na)
+    n.NA   <- apply(ipi, 1, n.is.na) == 1
+    n.NA2  <- apply(ipi, 1, n.is.na) == 2
+
+    ipi.hl <- rep(NA, length(n.NA))
+    ipi.hl[score %in% c(0, 1, 2)] <- 0
+    ipi.hl[score %in% c(3, 4, 5)] <- 1
+
+
+    ipi.hl2 <- rep(NA, length(n.NA))
+    ipi.hl2[score2 %in% c(0, 1, 2)] <- 0
+    ipi.hl2[score2 %in% c(3, 4, 5)] <- 1
+
+
+    ipi.hl[n.NA & score2 %in% c(0, 1, 3, 4) ] <-
+      ipi.hl2[n.NA & score2 %in% c(0, 1, 3, 4) ]
+
+    ipi.hl[n.NA2 & score2 %in% c(0, 3) ] <-
+      ipi.hl2[n.NA2 & score2 %in% c(0, 3) ]
+
+    return(list(ipi = score, ipi.hl = ipi.hl, na.1 = n.NA, ipi.na = score2))
+  }
+
+  metadata <- apply(meta_data, 2, as.character)
+  metadata <- as.data.frame(metadata[1:414, ], stringsAsFactors = FALSE)
+
+  GEO.ID <- metadata$geo_accession
+  id     <- gsub("Individual: ", "", metadata$source_name_ch1)
+  gender <- gsub("Gender: ",     "", metadata$characteristics_ch1)
+  age    <- gsub("Age: ",        "", metadata$characteristics_ch1.1)
+  tissue <- gsub("Tissue: ",     "", metadata$characteristics_ch1.2)
+
+  disease.state        <- gsub("Disease state: ",
+                               "", metadata$characteristics_ch1.3)
+  Submitting.diagnosis <- gsub("Clinical info: Submitting diagnosis: ",
+                               "", metadata$characteristics_ch1.5)
+  microarray.diagnosis <- gsub("Clinical info: Final microarray diagnosis: ",
+                               "", metadata$characteristics_ch1.6)
+  microarray.diagnosis <- gsub(" DLBCL", "", microarray.diagnosis)
+
+  status <- gsub("Clinical info: Follow up status: ",
+                 "", metadata$characteristics_ch1.7)
+  FU     <- gsub("Clinical info: Follow up years: ",
+                 "", metadata$characteristics_ch1.8)
+  chemo  <- gsub("Clinical info: Chemotherapy: ",
+                 "", metadata$characteristics_ch1.9)
+
+  chemo  <- gsub("-Like Regimen", "", chemo)
+
+  ECOG   <- gsub("Clinical info: ECOG performance status: ",
+                 "", metadata$characteristics_ch1.10)
+  stage  <- gsub("Clinical info: Stage: ",
+                 "", metadata$characteristics_ch1.11)
+  LDH    <- gsub("Clinical info: LDH ratio: ",
+                 "", metadata$characteristics_ch1.12)
+
+  No.Extra.Nodal <- gsub("Clinical info: Number of extranodal sites: ",
+                         "", metadata$characteristics_ch1.13)
+
+
+  metadataLLMPP <- data.frame(id, GEO.ID, gender, as.numeric(age), status,
+                              FU, chemo, tissue,
+                              disease.state, Submitting.diagnosis,
+                              microarray.diagnosis, ECOG, stage, LDH,
+                              No.Extra.Nodal = No.Extra.Nodal)
+
+  colnames(metadataLLMPP) <- c("id", "GEO.ID", "gender", "age",
+                               "survival.status", "FU", "chemo", "tissue",
+                               "disease.state", "Submitting.diagnosis",
+                               "microarray.diagnosis", "ECOG", "stage",
+                               "LDH", "No.Extra.Nodal")
+
+  metadataLLMPP$FU <- as.numeric(as.character(metadataLLMPP$FU))
+  metadataLLMPP$stage <- as.numeric(as.character(metadataLLMPP$stage))
+  metadataLLMPP$age   <- as.numeric(as.character(metadataLLMPP$age))
+  metadataLLMPP$No.Extra.Nodal <- as.numeric(as.character(metadataLLMPP$No.Extra.Nodal))
+  metadataLLMPP$ECOG <- as.numeric(as.character(metadataLLMPP$ECOG))
+  metadataLLMPP$LDH  <- as.numeric(as.character(metadataLLMPP$LDH))
+  ipi <- IPI(metadataLLMPP$age,   metadataLLMPP$ECOG,
+             metadataLLMPP$stage, metadataLLMPP$No.Extra.Nodal,
+             metadataLLMPP$LDH)
+
+  metadataLLMPP$ipi    <- as.factor(ipi$ipi)
+  metadataLLMPP$ipi.hl <- as.factor(ipi$ipi.hl)
+
+  metadataLLMPP$ipi.hl <- as.character(metadataLLMPP$ipi)
+  metadataLLMPP$ipi.hl[metadataLLMPP$ipi %in% c(0, 1)] <- "0-1"
+  metadataLLMPP$ipi.hl[metadataLLMPP$ipi %in% c(2, 3)] <- "2-3"
+  metadataLLMPP$ipi.hl[metadataLLMPP$ipi %in% c(4, 5)] <- "4-5"
+
+  metadataLLMPP$ipi.hl2 <- metadataLLMPP$ipi.hl
+
+  metadataLLMPP$ipi.hl2[ipi$ipi.na == 0 & ipi$na.1] <- "0-1"
+  metadataLLMPP$ipi.hl2[ipi$ipi.na == 2 & ipi$na.1] <- "2-3"
+  metadataLLMPP$ipi.hl2[ipi$ipi.na == 4 & ipi$na.1] <- "4-5"
+
+  # Creating survival objects
+  metadataLLMPP$OS <- survival::Surv(metadataLLMPP$FU,
+                                     metadataLLMPP$survival.status == "DEAD")
+
+  os5  <- ifelse(metadataLLMPP$FU > 5, 5, metadataLLMPP$FU)
+  ios5 <- pmin(ifelse(metadataLLMPP$FU > 5, 0, 1), metadataLLMPP$OS[,2])
+
+  metadataLLMPP$OS5  <- survival::Surv(as.numeric(os5), ios5)
+
+  metadataLLMPP$WrightClass  <- metadataLLMPP$microarray.diagnosis
+  metadataLLMPP$WrightClass2 <- as.character(metadataLLMPP$WrightClass)
+  metadataLLMPP$WrightClass2 <-
+    as.factor(gsub("Unclassified", "UC", metadataLLMPP$WrightClass2))
+
+  rownames(metadataLLMPP) <- paste(metadataLLMPP$GEO.ID, ".CEL",sep = "")
+
+  # Added factor describing the batches and CEL files
+  metadataLLMPP$Batch <- as.factor(metadataLLMPP$chemo)
+  metadataLLMPP$CEL   <- rownames(metadataLLMPP)
+  metadataLLMPP$GSM   <- as.character(metadataLLMPP$GEO.ID)
+
+  class(metadataLLMPP) <- class(meta_data)
+  return(metadataLLMPP)
+}