GatingHierarchy-class   Class GatingHierarchy
GatingSet,character,character-method
                        constructors for GatingSet
GatingSet-class         Class '"GatingSet"'
GatingSetList-class     Class '"GatingSetList"'
add,GatingSet,list-method
                        Create a GatingSet and add/remove the flowCore
                        gate(or population) to/from a
                        GatingHierarchy/GatingSet.
archive                 archive/unarchive to/from a tar file
booleanFilter-class     A class describing logical operation (& or |)
                        of the reference populations
clone                   clone a GatingSet
filterObject,rectangleGate-method
                        convert flowCore filter to a list
flowData,GatingSet-method
                        Fetch or replace the flowData object associated
                        with a GatingSet .
flowJoTrans             construct the flowJo-type biexponentioal
                        transformation function
flowJoWorkspace-class   An R representation of a flowJo workspace.
flowWorkspace-package   Import and replicate flowJo workspaces and
                        gating schemes using flowCore.
flowWorkspace.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
flowWorkspace.par.set   flowWorkspace.par.set sets a set of parameters
                        in the flowWorkspace package namespace.
getCompensationMatrices,GatingHierarchy-method
                        Retrieve the compensation matrices from a
                        GatingHierarchy
getData,GatingHierarchy,missing-method
                        get gated flow data from a
                        GatingHierarchy/GatingSet/GatingSetList
getFJWSubsetIndices     Fetch the indices for a subset of samples in a
                        flowJo workspace, based on a keyword value pair
getGate,GatingHierarchy,character-method
                        Return the flowCore gate definition associated
                        with a node in a GatingHierarchy/GatingSet.
getIndiceMat            Return the single-cell matrix of 1/0
                        dichotomized expression
getIndices,GatingHierarchy,character-method
                        Get the membership indices for each event with
                        respect to a particular gate in a
                        GatingHierarchy
getIndices,GatingSet,name-method
                        routine to return the indices by specify
                        boolean combination of reference nodes:
getKeywords,flowJoWorkspace,character-method
                        Get Keywords
getLoglevel             get/set the log level
getNodes,GatingSet-method
                        Get the names of all nodes from a gating
                        hierarchy.
getParent,GatingSet,character-method
                        Return the name of the parent population or a
                        list of child populations of the current
                        population in the GatingHierarchy
getProp,GatingHierarchy,character-method
                        Return a table of population statistics for all
                        populations in a GatingHierarchy/GatingSet or
                        the population proportions or the total number
                        of events of a node (population) in a
                        GatingHierarchy
getSample,GatingHierarchy-method
                        Get the sample name associated with a
                        GatingHierarchy
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
getSingleCellExpression,GatingSet,character-method
                        Return the cell events data that express in any
                        of the single populations defined in 'y'
getTransformations,GatingHierarchy-method
                        Return a list of transformations or a
                        transformation in a GatingHierarchy
insertGate              insert a dummy gate to the GatingSet
isNcdf                  determine the flow data associated with a
                        Gating Hiearchy is based on 'ncdfFlowSet' or
                        'flowSet'
keyword,GatingHierarchy,character-method
                        Retrieve a specific keyword for a specific
                        sample in a 'GatingHierarchy' or or set of
                        samples in a 'GatingSet' or 'GatingSetList'
lapply,GatingSet-method
                        apply 'FUN' to each sample (i.e.
                        'GatingHierarchy')
length,GatingSet-method
                        Methods to get the length of a GatingSet
mkformula               make a formula from a character vector
ncFlowSet               Fetch the flowData object associated with a
                        GatingSet .
openWorkspace,character-method
                        Open/Close a flowJo workspace
pData,GatingHierarchy-method
                        read/set pData of flow data associated with
                        'GatingSet' or 'GatingSetList'
parseWorkspace,flowJoWorkspace-method
                        Parse a flowJo Workspace
plot,GatingSet,missing-method
                        plot a gating tree
plotGate                Plot gates and associated cell population
                        contained in a 'GatingHierarchy' or 'GatingSet'
plotPopCV,GatingHierarchy-method
                        Plot the coefficient of variation between
                        flowJo and flowCore population statistics for
                        each population in a gating hierarchy.
prettyAxis              Determine tick mark locations and labels for a
                        given channel axis
recompute,GatingSet-method
                        Compute the cell events by the gates stored
                        within the gating tree
sampleNames,GatingHierarchy-method
                        Get/update sample names in a GatingSet
save_gs                 save/load a GatingSet/GatingSetList to/from
                        disk.
setGate,GatingHierarchy,character,filter-method
                        update the gate
setNode,GatingHierarchy,character,character-method
                        Update the name of one node in a gating
                        hierarchy/GatingSet.
subset.GatingSet        subset the GatingSet/GatingSetList based on
                        'pData'
transform,GatingSet-method
                        tranform the flow data asssociated with the
                        GatingSet
