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.
asinh_Gml2              inverse hyperbolic sine transform function
                        generator (GatingML 2.0 version)
asinhtGml2_trans        Inverse hyperbolic sine transformation.
booleanFilter-class     A class describing logical operation (& or |)
                        of the reference populations
checkRedundantNodes     try to determine the redundant terminal(or
                        leaf) nodes that can be removed
clone                   clone a GatingSet
compensate,GatingSet,ANY-method
                        compensate the flow data asssociated with the
                        GatingSet
dropRedundantChannels   Remove the channels from flow data that are not
                        used by gates
dropRedundantNodes      Remove the terminal leaf nodes that make the
                        gating trees to be different from one another.
estimateLogicle.GatingHierarchy
                        Compute logicle transformation from the
                        flowData associated with a GatingHierarchy
filterObject,rectangleGate-method
                        convert flowCore filter to a list It convert
                        the flowCore gate to a list whose structure can
                        be understood by underlying c++ data structure.
flowData,GatingSet-method
                        Fetch or replace the flowData object associated
                        with a GatingSet .
flowJo.fasinh           inverse hyperbolic sine transform function
flowJo.flog             flog transform function
flowJoTrans             construct the flowJo-type biexponentioal
                        transformation function
flowJoWorkspace-class   An R representation of a flowJo workspace.
flowJo_biexp_trans      flowJo biexponential transformation.
flowJo_fasinh_trans     flowJo inverse hyperbolic sine transformation.
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.
flow_breaks             Generate the breaks that makes sense for flow
                        data visualization
flow_trans              helper function to generate a trans objects
                        Used by other specific trans constructor
getCompensationMatrices,GatingHierarchy-method
                        Retrieve the compensation matrices from a
                        GatingHierarchy
getData,GatingHierarchy,missing-method
                        get gated flow data from a
                        GatingHierarchy/GatingSet/GatingSetList
getDescendants          get all the descendant nodes for the given
                        ancester
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
getMergedStats          Get Cell Population Statistics and Sample
                        Metadata
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
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,GatingSetList,character-method
                        Return the cell events data that express in any
                        of the single populations defined in 'y'
getStats                Exact MFI from populations(or nodes) for all
                        the markers
getTransformations,GatingHierarchy-method
                        Return a list of transformations or a
                        transformation in a GatingHierarchy
groupByChannels         split GatingSets into groups based on their
                        flow channels
groupByTree             split GatingSets into groups based on their
                        gating schemes Be careful that the splitted
                        resluts still points to the original data set!!
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
logicleGml2_trans       GatingML2 version of logicle transformation.
logicle_trans           logicle transformation.
logtGml2_trans          Gating-ML 2.0 Log transformation.
markernames,GatingHierarchy-method
                        Get/set the column(channel) or marker names
mkformula               make a formula from a character vector
moveNode                move a node along with all of its descendant
                        nodes to the given ancester
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 xml
                        and openCyto population statistics for each
                        population in a gating hierarchy.
pop.MFI                 built-in stats functions.
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.
set.count.xml           save the event counts parsed from xml into c++
                        tree structure
setGate,GatingHierarchy,character,filter-method
                        update the gate
setNode,GatingHierarchy,character,character-method
                        Update the name of one node in a gating
                        hierarchy/GatingSet.
standardize-GatingSet   The tools to standardize the tree structures
                        and channel names.
subset.GatingSet        subset the GatingSet/GatingSetList based on
                        'pData'
transform,GatingSet-method
                        tranform the flow data asssociated with the
                        GatingSet
transformerList         Constructor for transformerList object
updateChannels          Update the channel information of a GatingSet
                        (c++ part)
updateIndices,GatingHierarchy,character,logical-method
                        directly update event indices without changing
                        gates
