GatingHierarchy-class   Class GatingHierarchy
GatingSet-class         Class '"GatingSet"'
GatingSet-methods       constructors for GatingSet
GatingSetList-class     Class '"GatingSetList"'
[,GatingSet,ANY,ANY,ANY-method
                        Bracket operators on 'GatingSet' and
                        'GatingSetList' objects
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
cf_append_cols          Append data columns to a flowFrame
cf_backend_type         return the cytoframe backend storage format
cf_get_uri              Return the file path of the underlying h5 file
cf_is_subsetted         check whether a cytoframe/cytoset is a
                        subsetted(by column or by row) view
cf_write_disk           Save the cytoframe to disk
cf_write_h5             Save the cytoframe as h5 format
cf_write_tile           Save the cytoframe as h5 format
cleanup                 Remove on-disk files associatated with
                        flowWorkspace data classes
cleanup_temp            Remove temporary files associatated with
                        flowWorkspace data classes
compensate              compensate the flow data asssociated with the
                        GatingSet
convert                 Methods for conversion between flowCore and
                        flowWorkspace data classes
convert_backend         convert h5 based gs archive to tiledb
convert_legacy_gs       convert the legacy GatingSet archive (mixed
                        with R and C++ files) to the new format (C++
                        only)
cs_add_cytoframe        Add a cytoframe to a cytoset
cs_get_uri              Return the path of the underlying data files
cs_set_cytoframe        update a cytoframe in a cytoset
cytoctx                 Create cyto context that carries tiledb context
                        parameters
cytoframe               'cytoframe': A reference class for efficiently
                        managing the data representation of a
                        'flowFrame'
cytoframe-labels        Methods to change channel and marker names for
                        'cytoframe' and 'cytoset' objects
cytoset                 'cytoset': a reference class for efficiently
                        managing the data representation of a 'flowSet'
delete_gs               delete the archive of GatingSet
estimateLogicle         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.
filter_to_list          convert flowCore filter to a list It convert
                        the flowCore gate to a list whose structure can
                        be understood by underlying c++ data structure.
flowWorkspace-deprecated
                        Deprecated functions in package
                        'flowWorkspace'.
flowWorkspace-package   Import and replicate flowJo workspaces and
                        gating schemes using flowCore.
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
get_default_backend     get/set the default backend format of cytoframe
get_log_level           get/set the log level
gh_apply_to_cs          Construct a 'GatingSet' using a template
gh_apply_to_new_fcs     Construct a 'GatingSet' using a template and
                        FCS files
gh_copy_gate            Copy a node along with all of its descendant
                        nodes to the given ancestor
gh_get_cluster_labels   Retrieve the cluster labels from the cluster
                        nodes
gh_get_compensations    Retrieve the compensation matrices from a
                        'GatingHierarchy' or 'GatingSet'
gh_get_transformations
                        Return a list of transformations or a
                        transformation in a GatingHierarchy
gh_plot_pop_count_cv    Plot the coefficient of variation between xml
                        and openCyto population statistics for each
                        population in a gating hierarchy.
gh_pop_compare_stats    Compare the stats(count/freq) between the
                        version parsed from xml and the one
                        recalculated/gated from R
gh_pop_get_cluster_name
                        check if a node is clustering node
gh_pop_get_data         get gated flow data from a
                        GatingHierarchy/GatingSet/GatingSetList
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      Get the membership indices for each event with
                        respect to a particular gate in a
                        GatingHierarchy
gh_pop_get_indices_mat
                        Return the single-cell matrix of 1/0
                        dichotomized expression
gh_pop_get_proportion   Get count or proportion from populations
gh_pop_move             move a node along with all of its descendant
                        nodes to the given ancester
gh_pop_set_indices      directly update event indices without changing
                        gates
gh_pop_set_xml_count    save the event counts parsed from xml into c++
                        tree structure
gs_check_redundant_nodes
                        try to determine the redundant terminal(or
                        leaf) nodes that can be removed
gs_cyto_data            Fetch or replace the flowData object associated
                        with a GatingSet .
gs_get_compensation_internal
                        extract compensation object from GatingSet
gs_get_leaf_nodes       get all the leaf nodes
gs_get_pop_paths        Get the names of all nodes from a gating
                        hierarchy.
gs_get_singlecell_expression
                        Return the cell events data that express in any
                        of the single populations defined in 'y'
gs_is_persistent        determine whether the flow data associated with
                        a GatingSet is persistent(on-disk) or in-memory
gs_plot_diff_tree       visualize the tree structure differnece among
                        the GatingSets
gs_pop_add              Create a GatingSet and add/remove the flowCore
                        gate(or population) to/from a
                        GatingHierarchy/GatingSet.
gs_pop_get_count_fast   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
gs_pop_get_gate         Return the flowCore gate definition associated
                        with a node in a GatingHierarchy/GatingSet.
gs_pop_get_gs           subset gs by population node
gs_pop_get_parent       Return the name of the parent population or a
                        list of child populations of the current
                        population in the GatingHierarchy
gs_pop_get_stats        Extract stats from populations(or nodes)
gs_pop_get_stats_tfilter
                        Extract stats from populations(or nodes) within
                        a restricted time window
gs_pop_set_gate         update the gate
gs_pop_set_name         Update the name of one node in a gating
                        hierarchy/GatingSet.
gs_pop_set_visibility   hide/unhide a node
gs_remove_redundant_channels
                        Remove the channels from flow data that are not
                        used by gates
gs_remove_redundant_nodes
                        Remove the terminal leaf nodes that make the
                        gating trees to be different from one another.
gs_split_by_channels    split GatingSets into groups based on their
                        flow channels
gs_split_by_tree        split GatingSets into groups based on their
                        gating schemes Be careful that the splitted
                        resluts still points to the original data set!!
gs_update_channels      Update the channel information of a GatingSet
                        (c++ part)
gslist_to_gs            Merge a GatingSetList into a single GatingSet
identifier-methods      Retrieve/replace the GUID of a GatingSet or
                        GatingSetList
is_tiledb_support       check whether cytolib is build with tiledb
                        support
keyword                 Retrieve a specific keyword for a specific
                        sample in a 'GatingHierarchy' or or set of
                        samples in a 'GatingSet' or 'GatingSetList'
keyword-mutators        Methods to alter keywords in 'cytoframe',
                        'cytoset', 'GatingHierarchy', or 'GatingSet'
                        objects
lapply-methods          apply 'FUN' to each sample (i.e.
                        'GatingHierarchy' or 'cytoframe') in a
                        'GatingSet' or 'cytoset'
length                  Methods to get the length of a GatingSet
load_cytoframe          Load the cytoframe from disk
load_cytoframe_from_fcs
                        Read a single FCS file in to a cytoframe
load_cytoset_from_fcs   Read one or several FCS files in to a cytoset
load_meta               Flush/load meta data (keywords, pData,
                        channels/markers) to/from disk (only valid for
                        on-disk cytoset/cytoframe)
lock                    Lock/Unlock the cytoset/cytoframe by turning
                        on/off its read-only flag
logicleGml2_trans       GatingML2 version of logicle transformation.
logicle_trans           logicle transformation.
logtGml2_trans          Gating-ML 2.0 Log transformation.
markernames             Get/set the column(channel) or marker names
merge_list_to_gs        Merge a list of GatingSets into a single
                        GatingSet
ncFlowSet               Fetch the flowData object associated with a
                        GatingSet .
nodeflags               The flags of gate nodes
openWorkspace           It is now moved along with entire flowJo parser
                        to CytoML package
pData-methods           read/set pData of flow data associated with
                        'GatingHierarchy', 'GatingSet', or
                        'GatingSetList'
plot-methods            plot a gating tree
plotGate-methods-defunct
                        Plot gates and associated cell population
                        contained in a 'GatingHierarchy' or 'GatingSet'
pop_add                 Add populations to a GatingHierarchy
prettyAxis              Determine tick mark locations and labels for a
                        given channel axis
recompute               Compute the cell events by the gates stored
                        within the gating tree.
rotate_gate             Simplified geometric rotation of gates
                        associated with nodes
sampleNames             Get/update sample names in a GatingSet
save_cytoset            save/load a cytoset to/from disk.
                        load_cytoset() can load a cytoset from either
                        the archive previously saved by save_cytoset()
                        call or from a folder that contains a
                        collection of inidivudal cytoframe files
                        (either in h5 format or tiledb format)
save_gs                 save/load a GatingSet/GatingSetList to/from
                        disk.
scale_gate              Simplified geometric scaling of gates
                        associated with nodes
shift_gate              Simplified geometric translation of gates
                        associated with nodes
standardize-GatingSet   The tools to standardize the tree structures
                        and channel names.
stats.fun               built-in stats functions.
subset                  subset the GatingSet/GatingSetList based on
                        'pData'
swap_data_cols          Swap the colnames Perform some validity checks
                        before returning the updated colnames
transform               tranform the flow data asssociated with the
                        GatingSet
transform_gate          Simplified geometric transformations of gates
                        associated with nodes
transformerList         Constructor for transformerList object
