Hierarchical Gating Pipeline for flow cytometry data


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Documentation for package ‘openCyto’ version 1.0.14

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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
alias get gating method name
alias-method get gating method name
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 after standardizing and collapsing flowFrames
dims get gating method name
dims-method get gating method name
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.
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 Applies gatingTemplate to one GatingSet.
gating-method Applies gatingTemplate to one 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 get nodes from gatingTemplate object
getChildren-method get nodes from gatingTemplate object
getGate get nodes from gatingTemplate object
getGate-method get nodes from gatingTemplate object
getNodes get nodes from gatingTemplate object
getNodes-method get nodes from gatingTemplate object
getParent get nodes from gatingTemplate object
getParent-method get nodes from gatingTemplate object
groupBy get gating method name
groupBy-method get gating method name
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 get gating method name
isCollapse-method get gating method name
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
names get gating method name
names-method get gating method name
openCyto Hierarchical Gating Pipeline for flow cytometry data
parameters get gating method name
parameters-method get gating method name
plot plot a 'fcFilterList'
plot-method get nodes from gatingTemplate object
polyFunctions-class A class to represent a polyFunctions gating method.
posteriors get posteriors from a 'fcFilter' object
posteriors-method get posteriors from a 'fcFilter' object
ppMethod get nodes from gatingTemplate object
ppMethod-class A class to represent a preprocessing method.
ppMethod-method get nodes from gatingTemplate object
preprocessing apply a ppMethod to the 'GatingSet'
preprocessing-method apply a ppMethod to the 'GatingSet'
priors get priors from a 'fcFilter' object
priors-method get priors from a 'fcFilter' object
prior_flowClust Elicits data-driven priors from a flowSet object for specified channels
refGate-class A class to represent a reference gating method.
registerPlugins Register a gating or preprocessing function with OpenCyto
show a class storing the gating method and population information in a graphNEL object
show-method a class storing the gating method and population information in a graphNEL object
show-method A class to represent a gating method.
tailgate Gates the tail of a density using the derivative of a kernel density estimate after standardizing and collapsing flowFrames
templateGen generate a partially complete csv template from the existing gating hierarchy