CytoML.par.init         workspace version is parsed from xml node
                        '/Workspace/version' in flowJo workspace and
                        matched with this list to dispatch to the one
                        of the three workspace parsers
CytoML.par.set          CytoML.par.set sets a set of parameters in the
                        CytoML package namespace.
GatingSet,character,character-method
                        constructors for GatingSet
GatingSet2cytobank      Convert a GatingSet to a Cytobank-compatible
                        gatingML
GatingSet2flowJo        Convert a GatingSet to flowJo workspace
addCustomInfo           add customInfo nodes to each gate node and add
                        BooleanAndGates
compare.counts          compare the counts to cytobank's exported csv
                        so that the parsing result can be verified.
compensate,GatingSet,graphGML-method
                        compensate a GatingSet based on the
                        compensation information stored in graphGML
                        object
constructTree           Reconstruct the population tree from the
                        GateSets
cytobank2GatingSet.default
                        A wrapper that parse the gatingML and FCS files
                        (or cytobankExperiment object) into GatingSet
cytobankExperiment      Construct cytobankExperiment object from ACS
                        file
divaWorkspace-class     divaWorkspace class Inherited from
                        flowJoWorkspace-class
extend                  extend the gate to the minimum and maximum
                        limit of both dimensions based on the bounding
                        information.
flowJoWorkspace-class   An R representation of a flowJo workspace.
gating,graphGML,GatingSet-method
                        Apply the gatingML graph to a GatingSet
getChildren,graphGML,character-method
                        get children nodes
getCompensationMatrices.graphGML
                        Extract compensation from graphGML object.
getFJWSubsetIndices     Fetch the indices for a subset of samples in a
                        flowJo workspace, based on a keyword value pair
getGate,graphGML,character-method
                        get gate from the node
getKeywords,flowJoWorkspace,character-method
                        Get Keywords
getNodes,graphGML-method
                        get nodes from graphGML object
getParent,graphGML,character-method
                        get parent nodes
getSampleGroups,flowJoWorkspace-method
                        Get a table of sample groups from a flowJo
                        workspace
getSamples,flowJoWorkspace-method
                        Get a list of samples from a flowJo workspace
getTransformations.graphGML
                        Extract transformations from graphGML object.
graphGML-class          A graph object returned by
                        'read.gatingML.cytobank' function.
matchPath               Given the leaf node, try to find out if a
                        collection of nodes can be matched to a path in
                        a graph(tree) by the bottom-up searching
openDiva                open Diva xml workspace
openWorkspace.character
                        Open/Close a flowJo workspace
parse.gateInfo          Parse the cytobank custom_info for each gate
parseWorkspace,flowJoWorkspace-method
                        Parse a flowJo Workspace
plot,graphGML,missing-method
                        plot the population tree stored in graphGML.
range.GatingHierarchy   the parameter range from the flow data
                        associated with GatingHierarchy
read.gatingML.cytobank
                        Parser for gatingML exported by Cytobank
show,graphGML-method    show method for graphGML
