@@ -6,11 +6,13 @@

 #' @rdname cytobank2GatingSet

 #' @examples

 #' \dontrun{

-#' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

-#' fcsFiles <- list.files(pattern = "CytoTrol", 

-#'       system.file("extdata", package = "flowWorkspaceData"), full = TRUE)

-#' gs <- cytobank2GatingSet(xmlfile, fcsFiles)

-#' #plotGate(gs[[1]])

+#' acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")

+#' ce <- cytobankExperiment(acsfile)

+#' xmlfile <- ce$gatingML

+#' fcsFiles <- list.files(ce$fcsdir, full.names = TRUE)

+#' gs <<- cytobank2GatingSet(xmlfile, fcsFiles)

+#' library(ggcyto)

+#' autoplot(gs[[1]])

 #' }

 #' @importFrom flowWorkspace GatingSet transform

 #' @importFrom ncdfFlow read.ncdfFlowSet

@@ -42,12 +44,11 @@ cytobank2GatingSet.default <- function(x, FCS){

 #' @export compare.counts

 #' @examples

 #'

-#' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

-#' fcsFiles <- list.files(pattern = "CytoTrol", 

-#'         system.file("extdata", package = "flowWorkspaceData"), full = TRUE)

-#' gs <- cytobank2GatingSet(xmlfile, fcsFiles)

+#' acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")

+#' ce <- cytobankExperiment(acsfile)

+#' gs <- cytobank2GatingSet(ce)

 #' ## verify the stats are correct

-#' statsfile <- system.file("extdata/cytotrol_tcell_cytobank_counts.csv", package = "CytoML")

+#' statsfile <- ce$attachments[1]

 #' dt_merged <- compare.counts(gs, statsfile, id.vars = "population", skip = "FCS Filename")

 #' all.equal(dt_merged[, count.x], dt_merged[, count.y], tol = 5e-4)

 #'