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      A wrapper that parse the gatingML and FCS files
                        into GatingSet
extend                  extend the gate to the minimum and maximum
                        limit of both dimensions based on the bounding
                        information.
gating,graphGML,GatingSet-method
                        Apply the gatingML graph to a GatingSet
getChildren,graphGML,character-method
                        get children nodes
getCompensationMatrices,graphGML-method
                        Extract compensation from graphGML object.
getGate,graphGML,character-method
                        get gate from the node
getNodes,graphGML-method
                        get nodes from graphGML object
getParent,graphGML,character-method
                        get parent nodes
getTransformations,graphGML-method
                        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
parse.gateInfo          Parse the cytobank custom_info for each gate
plot,graphGML,missing-method
                        plot the population tree stored in graphGML.
read.gatingML.cytobank
                        Parser for gatingML exported by Cytobank
show,graphGML-method    show method for graphGML
