\name{flowWorkspace2flowCore}
\alias{flowWorkspace2flowCore}
\alias{flowWorkspace2flowCore-methods}
\alias{flowWorkspace2flowCore,flowJoWorkspace-method}
\alias{flowWorkspace2flowCore,GatingHierarchy-method}
\alias{flowWorkspace2flowCore,GatingSet-method}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
Convert the GatingHierarchies in a GatingSet to a flowCore workflow.
}
\description{
Extract the compensation matrices,transformation functions and 
 all the gates from GatingHierarchies in a GatingSet generated by the flowWorkspace package,
 and convert them to the respective views and actionItems of workFlows defined by flowCore package.
}
\usage{
\S4method{flowWorkspace2flowCore}{GatingSet}(obj, ...)
\S4method{flowWorkspace2flowCore}{GatingHierarchy}(obj, ...)
\S4method{flowWorkspace2flowCore}{flowJoWorkspace}(obj, ...)
}

\arguments{
  \item{obj}{
can be a \code{flowJoWorkspace},\code{GatingSet} or a \code{GatingHierarchy}
}
  \item{\dots}{
Additional arugments. 
\code{path="character"} a file path to the fcs file or files. 
\code{groupId="integer"} a number indicating which group of the data (FlowFrame) should be processed when obj is a flowJoWorkspace.
\code{isCompare} a logical flag indicating whether the gatingHierarchies should be compared and merged when they have the same structure if a flowJoWorkspace or GatingSet is provided as the input,default is TRUE    
}
}
\details{
When the function is applied to a flowJoWorkspace or GatingSet, it compares gating hierarchies and generate one workflow object for multiple samples if they have the same gating hierarchy structure.
When \code{obj} is a flowJoWorkspace it first calls parseWorkspace function to parse the Workspace and generate \code{GatingSet} object and then convert the GatingSet to workflows.  
}
\value{
Returns a workflow if \code{obj} is a GatingHierarchy.
Returns a list of workflows if \code{obj} is a flowJoWorkspace or a GatingSet.  
}
\references{
\url{http://www.rglab.org/}
}
\author{
Mike Jiang \email{wjiang2@fhcrc.org}
}

\seealso{
\code{\link{GatingSet-class}} \code{\link{GatingHierarchy-class}} \code{\link{flowJoWorkspace-class}} \code{\link{parseWorkspace}}
}
\examples{
##locate workspace xml file and fcs files
dataDir <- system.file("extdata", package = "flowWorkspace")
wsfile<-list.files(dataDir,pattern="xml",full=TRUE)[1]

##open workspace xml file
\dontrun{
ws<-openWorkspace(wsfile)

##Convert a flowWorkspace to workFlows 
wfs<-flowWorkspace2flowCore(ws,groupId=1,path=dataDir)
plotWf(wfs[[1]])

##parse workspace and convert a GatingSet to workFlows
G <- parseWorkspace(ws,execute=TRUE,name=1,path=dataDir)
wfs<-flowWorkspace2flowCore(G,isCompare=TRUE,path=dataDir)
plotWf(wfs[[1]])

##Convert a GatingHierarchy to workFlow
wf <- flowWorkspace2flowCore(G[[1]],path=dataDir)
plotWf(wf)
}
}
\keyword{ manip }