Class "fcReference" and its subclasses

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Description

Classes and methods to provide reference-based semantics for flow cytometry workflows.

Usage

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fcReference(ID=paste("genericRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcTreeReference(ID=paste("treeRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcAliasReference(ID=paste("aliasRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcDataReference(ID=paste("dataRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcActionReference(ID=paste("actionRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcViewReference(ID=paste("viewRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcFilterResultReference(ID=paste("fresRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcFilterReference(ID=paste("filterRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcCompensateReference(ID=paste("compRef",
                                           guid(), sep="_"),
                                  env=new.env(parent=emptyenv()))

fcNormalizationReference(ID=paste("normRef",
                                           guid(), sep="_"),
                                  env=new.env(parent=emptyenv()))

fcSubsettingReference(ID=paste("subRef",
                                           guid(), sep="_"),
                                  env=new.env(parent=emptyenv()))

fcTransformReference(ID=paste("transRef",
                                          guid(), sep="_"),
                                 env=new.env(parent=emptyenv()))

fcNullReference(...)


assign(x, value, pos = -1, envir = as.environment(pos), inherits = FALSE, 
    immediate = TRUE)

## S4 method for signature 'fcReference,missing,missing'
get(x, pos = -1, envir = as.environment(pos), mode = "any", 
    inherits = TRUE)

isNull(f)

Rm(symbol, envir, subSymbol, ...)

Arguments

x, f, symbol

An object of class or inheriting from class fcReference.

ID

The reference identifier.

value

An arbitrary R object which is supposed to be assigned to the environment in the workFlow object and to which a reference is returned.

env

An environment, usually within a workFlow object.

pos, envir

Objects of class workFlow.

inherits, immediate, mode, subSymbol, ...

Further arguments from the generics that are not used in this context.

Details

These classes provide references to objects within an R environment and allow for method dispatch based on the nature of the referenced object. The parent fcReference class is used for references to all R objects, unless there exists a more specific subclass. fcTreeReference, fcViewReference, and fcActionReference are used to reference to graphNEL, view, and actionItem objects, respectively. fcDataReference should be used for flowFrame or flowSet objects, whereas fcFilterResultReference, fcFilterReference, fcTransformReference, fcCompensateReference, and fcNormalizationReference link to filterResult, filter, transform and compensation objects. fsStructureReference only exists to jointly dispatch on certain subgroups of references.

Value

An object of class fcReference or one of its subclasses for the assign constructor.

The object referenced to for the get method.

A character string of the object symbol for the identifier method.

A logical scalar for the isNull method.

Extends

fcStructureReference:

Class "fcReference", directly.

fcTreeReference:

Class "fcStructureReference", directly. Class "fcReference", by class "fcStructureReference", distance 2.

fcAliasReference:

Class "fcStructureReference", directly. Class "fcReference", by class "fcStructureReference", distance 2.

fcDataReference:

Class "fcReference", directly.

fcActionReference:

Class "fcStructureReference", directly. Class "fcReference", by class "fcStructureReference", distance 2.

fcViewReference:

Class "fcStructureReference", directly. Class "fcReference", by class "fcStructureReference", distance 2.

fcFilterResultReference:

Class "fcReference", directly.

fcFilterReference:

Class "fcReference", directly.

fcCompensateReference:

Class "fcReference", directly.

fcTransformReference:

Class "fcReference", directly.

fcNormalizationReference:

Class "fcReference", directly.

fcNullReference:

Class "fcDataReference", directly. Class "fcActionReference", directly. Class "fcViewReference", directly. Class "fcFilterResultReference", directly. Class "fcFilterReference", directly. Class "fcCompensateReference", directly. Class "fcTransformReference", directly. Class "fcNormalizationReference", directly. Class "fcTreeReference", directly. Class "fcAliasReference", directly. Class "fcReference", by class "fcDataReference", distance2. Class "fcStructureReference", by class "fcActionReference", distance 2. Class "fcReference", by class "fcActionReference", distance 3. Class "fcStructureReference", by class "fcViewReference", distance 2. Class "fcReference", by class "fcViewReference", distance3. Class "fcReference", by class "fcFilterResultReference", distance 2. Class "fcReference", by class "fcFilterReference", distance 2. Class "fcReference", by class "fcCompensateReference", distance 2. Class "fcReference", by class "fcTransformReference", distance 2. Class "fcStructureReference", by class "fcTreeReference", distance 2. Class "fcReference", by class "fcTreeReference", distance 3.

Objects from the Class

Objects should be created via the assign constructor. Whenever an object is assigned to a workFlow using the assign method, an appropriate instance of class fcReference or one of its subclasses is returned. In addition, there are the usual constructor functions of same names as the classes that can be used for object instantiation without assignment. Note that this might lead to unresolvable references unless the object referenced to is available in the environment.

Slots

ID:

Object of class "character" The name of the object in env referenced to.

env:

Object of class "environment" An environment that contains the referenced objects. Usually, this will be the environment that's part of a workFlow object.

Methods

get

signature(x = "fcReference", pos = "missing", envir = "missing", mode = "missing", inherits = "missing"): Resolve the reference, i.e., get the object from the environment.

get

signature(x = "fcNullReference", pos = "missing", envir = "missing", mode = "missing", inherits = "missing"): Resolve the reference. This always returns NULL.

identifier

signature(object = "fcReference"): Return a character string of the object name.

isNull

signature(f = "fcReference"): Check whether a fcReference is a NULL reference. Note that this is different from a unresolvable reference.

Rm

signature(symbol = "fcReference", envir = "missing", subSymbol = "character"): Remove the object referenced to by a fcReference from its environment. The argument subSymbol will be automatically set by the generic and should never be provided by the user.

Rm

signature(symbol = "fcReference", envir = "workFlow", subSymbol = "character"): Remove the object referenced to by a fcReference from a workFlow. The argument subSymbol will be automatically set by the generic and should never be provided by the user.

Rm

signature(symbol = "fcNullReference", envir = "missing", subSymbol = "character"): Essentially, this doesn't do anything since there is no object referenced to.

show

signature(object = "fcReference"): Print details about the object.

show

signature(object = "fcNullReference"): Print details about the object.

Author(s)

Florian Hahne

See Also

workFlow

Examples

1
showClass("fcReference")

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