GatingHierarchy-class   Class GatingHierarchy
GatingSet,GatingHierarchy,character-method
                        constructors for GatingSet
GatingSet,flowSet,ANY-method
                        constructors for GatingSet
GatingSet-class         Class '"GatingSet"'
GatingSetList-class     Class '"GatingSetList"'
add                     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
compute_timestep        compute time step from fcs keyword
copyNode                Copy a node along with all of its descendant
                        nodes to the given ancestor
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
extract_cluster_pop_name_from_node
                        Extract the population name from the node path
                        It strips the parent path and cluster method
                        name.
filterObject            convert flowCore filter to a list It convert
                        the flowCore gate to a list whose structure can
                        be understood by underlying c++ data structure.
fix_channel_slash       toggle the channel names between '/' and '_'
                        character
flowData                Fetch or replace the flowData object associated
                        with a GatingSet .
flowWorkspace-deprecated
                        Deprecated functions in package
                        'flowWorkspace'.
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
flowjo_biexp            construct the flowJo-type biexponentioal
                        transformation function
flowjo_biexp_trans      flowJo biexponential transformation.
flowjo_fasinh           inverse hyperbolic sine transform function
flowjo_fasinh_trans     flowJo inverse hyperbolic sine transformation.
flowjo_log_trans        flog transform function
getCompensationMatrices
                        Retrieve the compensation matrices from a
                        GatingHierarchy
getData,GatingHierarchy-method
                        get gated flow data from a
                        GatingHierarchy/GatingSet/GatingSetList
getGate,GatingHierarchy,character-method
                        Return the flowCore gate definition associated
                        with a node in a GatingHierarchy/GatingSet.
getIndices,GatingHierarchy,character-method
                        Get the membership indices for each event with
                        respect to a particular gate in a
                        GatingHierarchy
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
getPopStats,GatingHierarchy-method
                        Compare the stats(count/freq) between the
                        version parsed from xml and the one
                        recalculated/gated from R
getPopStats,GatingSet-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
getProp                 Get count or proportion from populations
getSingleCellExpression
                        Return the cell events data that express in any
                        of the single populations defined in 'y'
getStats                Extract stats from populations(or nodes)
getTransformations      Return a list of transformations or a
                        transformation in a GatingHierarchy
get_log_level           get/set the log level
gh_get_cluster_labels   Retrieve the cluster labels from the cluster
                        nodes
gh_pop_get_cluster_name
                        check if a node is clustering node
gh_pop_get_descendants
                        get all the descendant nodes for the given
                        ancester
gh_pop_get_full_path    convert the partial gating path to the full
                        path
gh_pop_get_indices_mat
                        Return the single-cell matrix of 1/0
                        dichotomized expression
gh_pop_set_xml_count    save the event counts parsed from xml into c++
                        tree structure
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!!
gs_get_compensation_internal
                        extract compensation object from GatingSet
gs_get_leaf_nodes       get all the leaf nodes
gs_is_h5                determine the flow data associated with a
                        Gating Hiearchy is based on 'ncdfFlowSet' or
                        'flowSet'
gs_plot_diff_tree       visualize the tree structure differnece among
                        the GatingSets
gs_plot_pop_count_cv    Plot the coefficient of variation between xml
                        and openCyto population statistics for each
                        population in a gating hierarchy.
isGated                 The flags of gate nodes gh_pop_is_gated checks
                        if a node is already gated gh_pop_is_negated
                        checks if a node is negated. gh_pop_is_hidden
                        checks if a node is hidden.
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           It is now moved along with entire flowJo parser
                        to CytoML package
pData,GatingHierarchy-method
                        read/set pData of flow data associated with
                        'GatingSet' or 'GatingSetList'
plot,GatingSet,missing-method
                        plot a gating tree
plotGate                Plot gates and associated cell population
                        contained in a 'GatingHierarchy' or 'GatingSet'
pop.MFI                 built-in stats functions.
pop_add                 Add populations to a GatingHierarchy
prettyAxis              Determine tick mark locations and labels for a
                        given channel axis
rbind2,GatingSetList,missing-method
                        Merge a GatingSetList into a single GatingSet
recompute,GatingSet-method
                        Compute the cell events by the gates stored
                        within the gating tree.
rotate_gate             Simplified geometric rotation of gates
                        associated with nodes
sampleNames,GatingHierarchy-method
                        Get/update sample names in a GatingSet
save_gs                 save/load a GatingSet/GatingSetList to/from
                        disk.
scale_gate              Simplified geometric scaling of gates
                        associated with nodes
setGate                 update the gate
setNode,GatingHierarchy,character,character-method
                        Update the name of one node in a gating
                        hierarchy/GatingSet.
setNode,GatingHierarchy,character,logical-method
                        hide/unhide a node
shift_gate              Simplified geometric translation of gates
                        associated with nodes
standardize-GatingSet   The tools to standardize the tree structures
                        and channel names.
subset.GatingSet        subset the GatingSet/GatingSetList based on
                        'pData'
swap_data_cols          Swap the colnames Perform some validity checks
                        before returning the updated colnames
transform,GatingSet-method
                        tranform the flow data asssociated with the
                        GatingSet
transform_gate          Simplified geometric transformations of gates
                        associated with nodes
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
