.isPolyfunctional       A function to tell wether a gating method is
                        'polyFunctions'
.prior_flowClust1d      Elicits data-driven priors from a flowSet
                        object for a specified channel
.prior_kmeans           Elicits data-driven priors from a flowSet
                        object for specified channels using the K-Means
                        clustering algorithm
add,GatingHierarchy,ocRectangleGate-method
                        bypass the default flowWorkspace:::.addGate
add_pop                 apply a gating method to the 'GatingSet'
as.data.table.gatingTemplate
                        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
gating                  Apply the gates to a GatingSet
gating,gtMethod,GatingSet-method
                        apply a gtMethod to the 'GatingSet'
gatingTemplate-class    a class storing the gating method and
                        population information in a graphNEL object
getChildren,gatingTemplate,character-method
                        get children nodes
getGate,fcTree,character-method
                        get gates saved in 'fcTree'
getGate,gatingTemplate,character-method
                        get gating method from the node
getNodes,fcTree-method
                        get nodes from 'fcTree'
getNodes,gatingTemplate-method
                        get nodes from gatingTemplate object
getParent,gatingTemplate,character-method
                        get parent nodes
groupBy,gtMethod-method
                        get the grouping variable for the gating method
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
listgtMethods           Print a list of the registered gating methods
names,gtMethod-method   get gating method name
names,gtPopulation-method
                        get population name
ocRectRefGate           constructor for ocRectRefGate
ocRectRefGate-class     special gate type that mix the rectangleGate
                        with boolean gate
ocRectangleGate-class   the class that carries event indices as well
openCyto                Hierarchical Gating Pipeline for flow cytometry
                        data
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.
posteriors,fcFilter,ANY-method
                        get posteriors from a 'fcFilter' object
ppMethod,gatingTemplate,character-method
                        get preprocessing method from the node
ppMethod-class          A class to represent a preprocessing method.
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.
registerPlugins         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
templateGen             generate a partially complete csv template from
                        the existing gating hierarchy
toggle.helperGates      toggle/delete the hidden flag of the helper
                        gates
