R/normalize_batch.R

In anschue/toxprofileR: Functions for Retrieving Dynamic Toxicogenomic Fingerprints

#' Normalize Batch
#'
#' @param dslist list of EListRaw objects which should be normalized together
#' @param method string, normalization method (default: "cyclicloess")
#' @param output logical, if output plots should be given
#'
#' @return a list of EList objects containing the normalized data
#' @import limma
#' @export
#'
normalizeBatch <-
  function(dslist,
             method = "cyclicloess",
             output = T) {
    if (length(dslist) > 1) {
      # check if probe names are in the same order---------------------------------
      lapply(1:(length(dslist) - 1), function(id) {
        if (!identical(
          dslist[[id]]$genes$ProbeName,
          dslist[[id + 1]]$genes$ProbeName
        )) {
          stop("Probes not in the same order")
        }
      })

      common.dataframe <-
        do.call("cbind", lapply(dslist, function(ds) {
          ds[["E"]]
        }))

      if (output) {
        boxplot(log2(common.dataframe))
      }

      ## Normalize common dataframe
      common.cloess <-
        limma::normalizeBetweenArrays(log2(common.dataframe), method = method)

      if (output) {
        boxplot(common.cloess)
      }

      ## Write normalized data into single dataframes
      dslist_norm <- lapply(1:length(dslist), function(id) {
        start_id <-
          if (id == 1) {
            1
          } else {
            1 + sum(unlist(lapply(1:(
              id - 1
            ), function(x) {
              ncol(dslist[[x]][["E"]])
            })))
          }
        end_id <-
          sum(unlist(lapply(1:id, function(x) {
            ncol(dslist[[x]][["E"]])
          })))
        ds <- new("EList", lapply(dslist[[id]], function(x) {
          return(x)
        }))
        ds[["E"]] <- common.cloess[, start_id:end_id]
        return(ds)
      })
    } else {
      dslist_norm <-
        list(limma::normalizeBetweenArrays(dslist[[1]], method = method))
    }

    return(dslist_norm)
  }