Hierarchical Gating Pipeline for flow cytometry data


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Documentation for package ‘openCyto’ version 1.8.4

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openCyto-package Hierarchical Gating Pipeline for flow cytometry data
.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-method bypass the default flowWorkspace:::.addGate
add_pop apply a gating method to the 'GatingSet'
alias-method get population alias
as.data.table.gatingTemplate convert a gatingTemplate object to a data.table
boolMethod-class A class to represent a boolean gating method.
cytokine Gates the tail of a density using the derivative of a kernel density estimate
dims-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.
filterObject-method construct logicalGate obj
flowClust.1d Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters.
flowClust.2d Automatic identification of a population of interest via flowClust based on two markers
gating-method apply a 'boolMethod' to the 'GatingSet'
gating-method apply a gtMethod to the 'GatingSet'
gating-method Applies gatingTemplate to one GatingSet.
gating-method apply a 'polyFunctions' gating method to the 'GatingSet'
gating-method apply a 'refGate' to the 'GatingSet'
gatingTemplate a class storing the gating method and population information in a graphNEL object
gatingTemplate-class a class storing the gating method and population information in a graphNEL object
gatingTemplate-method a class storing the gating method and population information in a graphNEL object
getChildren-method get children nodes
getGate-method get gates saved in 'fcTree'
getGate-method get gating method from the node
getNodes-method get nodes from 'fcTree'
getNodes-method get nodes from gatingTemplate object
getParent-method get parent nodes
groupBy-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-method get the flag that determines whether gating method is applied on collapsed data
listgtMethods Print a list of the registered gating methods
mindensity Determines a cutpoint as the minimum point of a kernel density estimate between two peaks
mindensity2 An improved version of mindensity used to determines a cutpoint as the minimum point of a kernel density estimate between two peaks.
names-method get gating method name
names-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
parameters-method get parameters of the gating method/function
plot-method plot a 'fcFilterList'
plot-method plot the flowClust gating results
plot-method plot the gating scheme
polyFunctions-class A class to represent a polyFunctions gating method.
posteriors-method get posteriors from a 'fcFilter' object
ppMethod-class A class to represent a preprocessing method.
ppMethod-method get preprocessing method from the node
preprocessing-method apply a ppMethod to the 'GatingSet'
priors-method get priors from a 'fcFilter' object
prior_flowClust Elicits data-driven priors from a flowSet object for specified channels
quadGate.seq sequential quadrant gating function
quadGate.tmix quadGate based on flowClust::tmixFiler
refGate-class A class to represent a reference gating method.
registerGatingFunction Register a gating or preprocessing function with OpenCyto
registerPlugins Register a gating or preprocessing function with OpenCyto
show-method show method for boolMethod
show-method show method for fcFilter
show-method show method for gatingTemplate
show-method show method for gtMethod
tailgate Gates the tail of a density using the derivative of a kernel density estimate
templateGen generate a partially complete csv template from the existing gating hierarchy