ExportTSVAnalysis       Export a GatingSet as a set of TSV (tab
                        separated value) files for statistics, gates,
                        and plots.
GatingHierarchy-class   Class '"GatingHierarchy"'
GatingSet-class         Class '"GatingSet"'
closeWorkspace          Close a flowJoWorkspace
ellipsoidGate2FlowJoVertices
                        Get the vertices of an ellipsoid gate needed to
                        export it to flowJo
execute                 Apply the GatingHierarchy to data, computing
                        population statistics along the way.
exportAsFlowJoXML       Export a workFlow to FlowJo XML
flowJoWorkspace-class   Class '"flowJoWorkspace"'
flowWorkspace-package   Import and replicate flowJo workspaces and
                        gating schemes using flowCore.
flowWorkspace2flowCore
                        Convert the GatingHierarchies in a GatingSet to
                        a flowCore workflow.
getBoundaries           Get the boundaries of a flowJo gate
getChildren             Returns a list of child populations of the
                        current node in the 'GatingHierarchy'
getCompensationMatrices
                        Retrieve the compensation matrices from a
                        flowJo Workspace
getData                 Return the flowFrame associated with a
                        GatingHierarchy
getDimensions           Return the dimensions on which a gate is
                        applied within a GatingHierarchy
getFJWSubsetIndices     Fetch the indices for a subset of samples in a
                        flowJo workspace, based on a keyword value pair
getGate                 Return the flowCore gate definition associated
                        with a node in a GatingHierarchy.
getIndiceFile           Returns the .nc file used to store the gating
                        indices for the GatingHierarchy
getIndices              Get the membership indices for each event with
                        respect to a particular gate in a
                        GatingHierarchy
getKeywords             Get List of Keywords for a Flow Sample
getNcdf                 Return the ncdfFlow object storing the data
getNodes                Get the names of all nodes in a gating
                        hierarchy
getParent               Return the name of the parent population of the
                        current population in the GatingHierarchy
getPopStats             Return a table of population statistics for all
                        populations in a GatingHierarchy
getProp                 Get the population proportions of a node
                        (population) in a GatingHierarchy
getSample               Get the sample name associated with a
                        GatingHierarchy
getSampleGroups         Get a table of sample groups from a flowJo
                        workspace
getSamples              Get a list of samples in a flowJo workspace or
                        a GatingSet
getTotal                Fetch the total number of events in a gate
                        defined in a GatingHierarchy
getTransformations      Return a list of transformations in a flowJo
                        workspace
haveSameGatingHierarchy
                        Tests whether two GatingHierarchy or GatingSet
                        objects have the same gating structure.
includedChannel2ExcludedChannel
                        Convert a list of parameter names in a
                        'GatingSet' to its complement.
includedGate2ExcludedGate
                        Convert a set of gates given by their flowJo
                        gate paths to its complement (and excluding
                        Boolean gates), referenced by gate indices
                        recognized by 'normalizeGatingSet'.
keyword                 Methods to retrieve keywords associated with an
                        FCS sample
lapply-methods          Methods for iterating over a gating set
length-methods          Methods to get the length of a GatingSet
openWorkspace           Open a flowJo workspace
parseWorkspace          Parse a flowJo Workspace
plot                    Plot a GatingHierarchy
plotGate                Plot a flowJo Gate and Cell Population
plotPopCV               Plot the coefficient of variation between
                        flowJo and flowCore population statistics for
                        each population in a gating hierarchy.
plotWf                  plot a workflow
recomputeGatingSet      Recalculates all the gating in the GatingSet if
                        netCDF storage is used.
saveNcdf                Save the netcdf file of a GatingSet or
                        GatingHierarchy to a permanent location.
summary-methods         Summarize a flowJoWorkspace object
