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openCyto (version 1.10.3)

Hierarchical Gating Pipeline for flow cytometry data

Description

This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

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Version

Version

1.10.3

License

Artistic-2.0

Maintainer

MJiang

Last Published

February 15th, 2017

Functions in openCyto (1.10.3)

fcEllipsoidGate

constuctor for fcEllipsoidGate
filterObject,logicalFilterResult-method

construct logicalGate obj
gatingTemplate-class

a class storing the gating method and population information in a graphNEL object
fcFilterList

constuctor for fcFilterList
dummyMethod-class

A class to represent a dummy gating method that does nothing but serves as reference to be refered by other population
fcTree

constructor of fcTree
gating,refGate,GatingSet-method

apply a refGate to the GatingSet
add,GatingHierarchy,multipleFilterResult-method

bypass the default flowWorkspace:::.addGate
gating,gtMethod,GatingSet-method

apply a gtMethod to the GatingSet
names,gtMethod-method

get gating method name
gating,boolMethod,GatingSet-method

apply a boolMethod to the GatingSet
getGate,gatingTemplate,character-method

get gating method from the node
ocRectangleGate-class

the class that carries event indices as well
names,gtPopulation-method

get population name
fcRectangleGate-class

a concrete class that reprents the rectangleGate generated by flowClust
parameters,gtMethod-method

get parameters of the gating method/function
plot,fcTree,character-method

plot the flowClust gating results
.prior_flowClust1d

Elicits data-driven priors from a flowSet object for a specified channel
show,boolMethod-method

show method for boolMethod
prior_flowClust

Elicits data-driven priors from a flowSet object for specified channels
fcRectangleGate

constuctor for fcRectangleGate
preprocessing,ppMethod,GatingSet-method

apply a ppMethod to the GatingSet
show,fcFilter-method

show method for fcFilter
show,gatingTemplate-method

show method for gatingTemplate
getGate,fcTree,character-method

get gates saved in fcTree
getParent,gatingTemplate,character-method

get parent nodes
fcFilter-class

a virtual class that represents the gating result generated by flowClust gating function
gating,polyFunctions,GatingSet-method

apply a polyFunctions gating method to the GatingSet
as.data.table.gatingTemplate

convert a gatingTemplate object to a data.table
fcEllipsoidGate-class

a concrete class that reprents the ellipsoidGate generated by flowClust
gtMethod-class

A class to represent a gating method.
ocRectRefGate-class

special gate type that mix the rectangleGate with boolean gate
listgtMethods

Print a list of the registered gating methods
getNodes,fcTree-method

get nodes from fcTree
priors,fcFilter,ANY-method

get priors from a fcFilter object
getChildren,gatingTemplate,character-method

get children nodes
show,gtMethod-method

show method for gtMethod
refGate-class

A class to represent a reference gating method.
fcPolygonGate

constuctor for fcPolygonGate
gating

Apply the gates to a GatingSet
isCollapse,gtMethod-method

get the flag that determines whether gating method is applied on collapsed data
tailgate

Gates the tail of a density using the derivative of a kernel density estimate
ppMethod-class

A class to represent a preprocessing method.
flowClust.2d

Automatic identification of a population of interest via flowClust based on two markers
plot,fcFilterList,ANY-method

plot a fcFilterList
templateGen

generate a partially complete csv template from the existing gating hierarchy
registerPlugins

Register a gating or preprocessing function with OpenCyto
getNodes,gatingTemplate-method

get nodes from gatingTemplate object
quantileGate

Determine the cutpoint by the events quantile.
add_pop

apply a gating method to the GatingSet
dims,gtMethod-method

get gating method dimensions
mindensity

Determines a cutpoint as the minimum point of a kernel density estimate between two peaks
.isPolyfunctional

A function to tell wether a gating method is polyFunctions
posteriors,fcFilter,ANY-method

get posteriors from a fcFilter object
ppMethod,gatingTemplate,character-method

get preprocessing method from the node
openCyto

Hierarchical Gating Pipeline for flow cytometry data
plot,gatingTemplate,missing-method

plot the gating scheme
groupBy,gtMethod-method

get the grouping variable for the gating method
fcTree-class

A class to represent a flowClust tree.
gtSubsets-class

A class representing a group of cell populations.
ocRectRefGate

constructor for ocRectRefGate
mindensity2

An improved version of mindensity used to determines a cutpoint as the minimum point of a kernel density estimate between two peaks.
quadGate.seq

sequential quadrant gating function
polyFunctions-class

A class to represent a polyFunctions gating method.
boolMethod-class

A class to represent a boolean gating method.
fcFilterList-class

a class that extends filterList class.
flowClust.1d

Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters.
fcPolygonGate-class

a concrete class that reprents the polygonGate generated by flowClust
gtPopulation-class

A class to represent a cell population that will be generated by a gating method.
quadGate.tmix

quadGate based on flowClust::tmixFiler
.prior_kmeans

Elicits data-driven priors from a flowSet object for specified channels using the K-Means clustering algorithm