R/ComBat.step2.R

In ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

#' Perform the second step of ComBat
#'
#' The first ComBat step (on the signatures only) has already been
#' performed. This step performs batch correction on the test data,
#' using reference batch ComBat, to prepare the test data for ASSIGN
#' analysis.
#'
#' This function downloads the training data from the internet, so an internet
#' connection is necessary
#'
#' @param testData The input test data to batch correct
#' @param pcaPlots a logical value indicating whether or not the function
#' should create PCA plots. The default is FALSE.
#' @param combat_train the ComBat training data data frame. If you do not have
#' this, the function will attempt to download it from the internet. Please
#' contact the developers if you have any issues with access to the file.
#' @param plots_to_console By default this function will write PDF versions of
#' the plots. Set this to TRUE to send the plots to the command line. The
#' default is FALSE.
#'
#' @return A list of data.frames is returned, including control (GFP) and
#' signature data, as well as the batch corrected test data. This data can go
#' directly into the runassign.single and runassign.multi functions, or
#' subsetted to go directly into ASSIGN.
#'
#' @export ComBat.step2
ComBat.step2 <- function(testData, pcaPlots=FALSE, combat_train=NULL,
                         plots_to_console=FALSE) {
  if (!("ref.batch" %in% names(as.list(args(sva::ComBat))))) {
    stop("Installed version of sva: ", utils::packageVersion("sva"), " does not have ref.batch option.\n",
         "Use devtools to install the github version of sva:\ndevtools::install_github('jtleek/sva-devel')")
  }
  if (is.null(combat_train)) {
    combat_train_file <- tempfile(pattern = "combat_train", fileext = ".rda")
    utils::download.file("https://drive.google.com/uc?authuser=0&id=1juOofXauICxkiEl8agpRueRy7rK86nA_&export=download",
                         combat_train_file)
    load(combat_train_file)
    unlink(combat_train_file)
    rm(combat_train_file)
  }

  dat <- merge_drop(combat_train, testData)
  sub <- c(rep("gfp_egfr", 6),
           rep("egfr", 6),
           rep("gfp", 12),
           rep("akt", 6),
           rep("bad", 6),
           rep("her2", 5),
           rep("igf1r", 6),
           rep("raf", 6),
           rep("gfp_kras", 9),
           rep("krasgv", 9),
           rep("test", ncol(testData)))
  bat <- c(rep(1, ncol(combat_train)), rep(2, ncol(testData)))
  if (pcaPlots) {
    pcaplotbefore <- pcaplot(dat, sub, plottitle = "PCA: Before ComBat")
    if (plots_to_console) {
      print(pcaplotbefore)
    }
    grDevices::pdf("pca_refcombat_twostep.pdf")
    print(pcaplotbefore)
  }
  combat_expr1 <- sva::ComBat(dat = as.matrix(dat), batch = bat, mod = NULL, ref.batch = 1)
  if (pcaPlots) {
    pcaplotafter <- pcaplot(combat_expr1, sub, plottitle = "PCA: After ComBat")
    print(pcaplotafter)
    invisible(grDevices::dev.off())
    if (plots_to_console) {
      print(pcaplotafter)
    }
  }
  c_gfp      <- combat_expr1[, 13:24]
  c_akt      <- combat_expr1[, 25:30]
  c_bad      <- combat_expr1[, 31:36]
  c_her2     <- combat_expr1[, 37:41]
  c_igf1r    <- combat_expr1[, 42:47]
  c_raf      <- combat_expr1[, 48:53]
  c_egfr_gfp <- combat_expr1[, 1:6]
  c_egfr     <- combat_expr1[, 7:12]
  c_kras_gfp <- combat_expr1[, 54:62]
  c_krasgv   <- combat_expr1[, 63:71]
  c_test     <- combat_expr1[, (ncol(combat_train) + 1):ncol(combat_expr1)]
  results <- list(gfp = c_gfp, akt = c_akt, bad = c_bad, her2 = c_her2,
                  igf1r = c_igf1r, raf = c_raf, egfr_gfp = c_egfr_gfp,
                  egfr = c_egfr, kras_gfp = c_kras_gfp, krasgv = c_krasgv,
                  test = c_test)
  return(results)
}