fcReference-class {flowCore} | R Documentation |
Classes and methods to provide reference-based semantics for flow cytometry workflows.
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, ...)
x, f, symbol |
An object of class or inheriting from class
|
ID |
The reference identifier. |
value |
An arbitrary R object which is supposed to be assigned to the
environment in the |
env |
An environment, usually within a |
pos, envir |
Objects of class |
inherits, immediate, mode, subSymbol, ... |
Further arguments from the generics that are not used in this context. |
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.
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.
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.
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 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.
signature(x = "fcReference", pos = "missing", envir
= "missing", mode = "missing", inherits = "missing")
: Resolve
the reference, i.e., get the object from the environment.
signature(x = "fcNullReference", pos = "missing",
envir = "missing", mode = "missing", inherits = "missing")
: Resolve
the reference. This always returns NULL
.
signature(object = "fcReference")
: Return
a character string of the object name.
signature(f = "fcReference")
: Check whether a
fcReference
is a NULL
reference. Note that this is
different from a unresolvable reference.
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.
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.
signature(symbol = "fcNullReference", envir =
"missing", subSymbol = "character")
: Essentially, this doesn't do
anything since there is no object referenced to.
signature(object = "fcReference")
: Print details
about the object.
signature(object = "fcNullReference")
: Print details
about the object.
Florian Hahne
showClass("fcReference")