@@ -1,7 +1,7 @@

 Package: flowWorkspace

 Type: Package

 Title: Infrastructure for representing and interacting with the gated cytometry

-Version: 3.27.25

+Version: 3.27.26

 Date: 2011-06-10

 Author: Greg Finak, Mike Jiang

 Maintainer: Greg Finak <gfinak@fhcrc.org>,Mike Jiang <wjiang2@fhcrc.org>

@@ -61,8 +61,8 @@ getStats.GatingSet <- function(x, ...){

 #'          when character, it is expected to be either "count" or "percent". Default is "count" (total number of events in the populations).

 #'          when a function,  it takes a flowFrame object through 'fr' argument and return the stats as a named vector.

 #' @param inverse.transform logical flag . Whether inverse transform the data before computing the stats.

-

-getStats.GatingHierarchy <- function(x, nodes = NULL, type = "count", inverse.transform = FALSE, ...){

+#' @param stats.fun.arg a list of arguments passed to `type` when 'type' is a function.

+getStats.GatingHierarchy <- function(x, nodes = NULL, type = "count", inverse.transform = FALSE, stats.fun.arg = list(), ...){

   gh <- x

   if(is.null(nodes))

     nodes <- getNodes(gh, ...)

@@ -90,7 +90,10 @@ getStats.GatingHierarchy <- function(x, nodes = NULL, type = "count", inverse.tr

         trans <- transformList(names(trans), trans)

         fr <- transform(fr, trans)

       }

-      res <- type(fr)

+      thisCall <- quote(type(fr))

+      thisCall <- as.call(c(as.list(thisCall), stats.fun.arg))

+      

+      res <- eval(thisCall)

     }

     as.data.table(t(res))

@@ -14,7 +14,7 @@ getStats(x, ...)

 \method{getStats}{GatingSet}(x, ...)

 \method{getStats}{GatingHierarchy}(x, nodes = NULL, type = "count",

-  inverse.transform = FALSE, ...)

+  inverse.transform = FALSE, stats.fun.arg = list(), ...)

 }

 \arguments{

 \item{x}{a GatingSet or GatingHierarchy}

@@ -29,6 +29,8 @@ when character, it is expected to be either "count" or "percent". Default is "co

 when a function,  it takes a flowFrame object through 'fr' argument and return the stats as a named vector.}

 \item{inverse.transform}{logical flag . Whether inverse transform the data before computing the stats.}

+

+\item{stats.fun.arg}{a list of arguments passed to `type` when 'type' is a function.}

 }

 \value{

 a data.table that contains MFI values for each marker per column along with 'pop' column and 'sample' column (when used on a 'GatingSet')