as.data.table           convert a gatingTemplate object to a data.table
boolMethod-class        A class to represent a boolean gating method.
dims,gtMethod-method    get gating method dimensions
dummyMethod-class       A class to represent a dummy gating method that
                        does nothing but serves as reference to be
                        refered by other population
fcEllipsoidGate         constuctor for 'fcEllipsoidGate'
fcEllipsoidGate-class   a concrete class that reprents the
                        ellipsoidGate generated by flowClust
fcFilter-class          a virtual class that represents the gating
                        result generated by flowClust gating function
fcFilterList            constuctor for 'fcFilterList'
fcFilterList-class      a class that extends 'filterList' class.
fcPolygonGate           constuctor for 'fcPolygonGate'
fcPolygonGate-class     a concrete class that reprents the polygonGate
                        generated by flowClust
fcRectangleGate         constuctor for 'fcRectangleGate'
fcRectangleGate-class   a concrete class that reprents the
                        rectangleGate generated by flowClust
fcTree                  constructor of 'fcTree'
fcTree-class            A class to represent a flowClust tree.
gate_flowclust_1d       Applies flowClust to 1 feature to determine a
                        cutpoint between the minimum cluster and all
                        other clusters.
gate_flowclust_2d       Automatic identification of a population of
                        interest via flowClust based on two markers
gate_mindensity         Determines a cutpoint as the minimum point of a
                        kernel density estimate between two peaks
gate_mindensity2        An improved version of mindensity used to
                        determines a cutpoint as the minimum point of a
                        kernel density estimate between two peaks.
gate_quad_sequential    sequential quadrant gating function
gate_quad_tmix          quadGate based on flowClust::tmixFiler
gate_quantile           Determine the cutpoint by the events quantile.
gate_tail               Gates the tail of a density using the
                        derivative of a kernel density estimate
gatingTemplate-class    a class storing the gating method and
                        population information in a graphNEL object
getGate,fcTree,character-method
                        get gates saved in 'fcTree'
getNodes,fcTree-method
                        get nodes from 'fcTree'
gh_generate_template    generate a partially complete csv template from
                        the existing gating hierarchy
groupBy,gtMethod-method
                        get the grouping variable for the gating method
gs_add_gating_method    apply a gating method to the 'GatingSet'
gs_add_gating_method_init
                        Clear history of 'gs_add_gating_method' calls
                        for a given 'GatingSet' or 'GatingSetList'
gs_remove_gating_method
                        Reverse the action of gating methods applied
                        via 'gs_add_gating_method'
gt_gating               Applies a gatingTemplate to a GatingSet.
gt_get_children         get children nodes
gt_get_gate             get gating method from the node
gt_get_nodes            get nodes from gatingTemplate object
gt_get_parent           get parent nodes
gt_list_methods         Print a list of the registered gating methods
gt_toggle_helpergates   toggle/delete the hidden flag of the helper
                        gates
gtMethod-class          A class to represent a gating method.
gtPopulation-class      A class to represent a cell population that
                        will be generated by a gating method.
gtSubsets-class         A class representing a group of cell
                        populations.
isCollapse,gtMethod-method
                        get the flag that determines whether gating
                        method is applied on collapsed data
names,gtMethod-method   get gating method name
names,gtPopulation-method
                        get population name
ocRectangleGate-class   the class that carries event indices as well
ocRectRefGate           constructor for ocRectRefGate
ocRectRefGate-class     special gate type that mix the rectangleGate
                        with boolean gate
openCyto                Hierarchical Gating Pipeline for flow cytometry
                        data
openCyto-deprecated     Deprecated functions in package 'openCyto'.
openCyto.options        Some global options for openCyto See examples
                        for the meaning of these options and how to
                        get/set them.
parameters,gtMethod-method
                        get parameters of the gating method/function
plot,fcFilterList,ANY-method
                        plot a 'fcFilterList'
plot,fcTree,character-method
                        plot the flowClust gating results
plot,gatingTemplate,missing-method
                        plot the gating scheme
polyFunctions-class     A class to represent a polyFunctions gating
                        method.
pop_add.ocRectangleGate
                        bypass the default flowWorkspace:::.addGate
posteriors,fcFilter,ANY-method
                        get posteriors from a 'fcFilter' object
ppMethod-class          A class to represent a preprocessing method.
ppMethod,gatingTemplate,character-method
                        get preprocessing method from the node
preprocessing,ppMethod,GatingSet-method
                        apply a ppMethod to the 'GatingSet'
prior_flowclust         Elicits data-driven priors from a flowSet
                        object for specified channels
priors,fcFilter,ANY-method
                        get priors from a 'fcFilter' object
refGate-class           A class to represent a reference gating method.
register_plugins        Register a gating or preprocessing function
                        with OpenCyto
show,boolMethod-method
                        show method for boolMethod
show,fcFilter-method    show method for fcFilter
show,gatingTemplate-method
                        show method for gatingTemplate
show,gtMethod-method    show method for gtMethod
tautstring              Taut String Density Estimator Gating
