R/batch.R

In flowSpy: A Toolkit for Flow And Mass Cytometry Data

#'
#' correctBatchFSPY
#'
#' @description
#' Remove batch effect in FSPY object
#' @param object An FSPY object
#' @param batch vector. Batch covariate (only one batch allowed)
#' @param par.prior logical. TRUE indicates parametric adjustments will be used,
#'    FALSE indicates non-parametric adjustments will be used.
#' @param mean.only logical. FALSE If TRUE ComBat only corrects the mean of the batch
#'    effect (no scale adjustment)
#' @param verbose logical. Whether to show log information
#' @param ... Parameters passing to \code{\link[sva]{ComBat}} function
#'
#' @seealso \code{\link[BiocNeighbors]{findKNN}}
#'
#' @return An FSPY object after removing batch effect
#'
#' @importFrom sva ComBat
#' @export
#'
#' @return An FSPY object with corrected batch effects
#' @examples
#'
#' if (FALSE) {
#'   plot.meta <- fetchPlotMeta(fspy)
#'   batch <- as.numeric(plot.meta$stage)
#'   fspy <- correctBatchFSPY(object, batch = batch)
#' }
#'
correctBatchFSPY <- function(object, batch = NULL, par.prior = TRUE,
                             mean.only = TRUE, verbose = FALSE, ...) {
  log.data <- object@log.data

  # correct batch effect using ComBat
  log.data.combat <- sva::ComBat(dat = t(log.data), batch = batch,
                                 par.prior = par.prior,
                                 mean.only = mean.only, ...)

  object@log.data <- t(log.data.combat)
  return(object)
}