Description Usage Arguments Details Value See Also Examples
updateObject
is a generic function that returns an instance
of object
updated to its current class definition.
1 2 3 4 5 | updateObject(object, ..., verbose=FALSE)
## Related utilities:
updateObjectFromSlots(object, objclass=class(object), ..., verbose=FALSE)
getObjectSlots(object)
|
object |
Object to be updated for Object for slot information to be extracted from for
|
... |
Additional arguments, for use in specific |
verbose |
|
objclass |
Optional character string naming the class of the object to be created. |
Updating objects is primarily useful when an object has been serialized (e.g., stored to disk) for some time (e.g., months), and the class definition has in the mean time changed. Because of the changed class definition, the serialized instance is no longer valid.
updateObject
requires that the class of the returned object be
the same as the class of the argument object
, and that the
object is valid (see validObject
). By default,
updateObject
has the following behaviors:
updateObject(ANY, ..., verbose=FALSE)
By default, updateObject
uses heuristic methods to determine
whether the object should be the ‘new’ S4 type (introduced in R 2.4.0),
but is not. If the heuristics indicate an update is required,
the updateObjectFromSlots
function tries to update the
object. The default method returns the original S4 object or the
successfully updated object, or issues an error if an update is
required but not possible.
The optional named argument verbose
causes a message to be
printed describing the action.
Arguments ...
are passed to updateObjectFromSlots
.
updateObject(list, ..., verbose=FALSE)
Visit each element in list
, applying
updateObject(list[[elt]], ..., verbose=verbose)
.
updateObject(environment, ..., verbose=FALSE)
Visit each element in environment
, applying
updateObject(environment[[elt]], ..., verbose=verbose)
updateObject(formula, ..., verbose=FALSE)
Do nothing; the environment of the formula may be too general
(e.g., R_GlobalEnv
) to attempt an update.
updateObject(envRefClass, ..., verbose=FALSE)
Attempt to update objects from fields using a strategy like
updateObjectFromSlots
Method 1.
updateObjectFromSlots(object, objclass=class(object), ...,
verbose=FALSE)
is a utility function that identifies the intersection
of slots defined in the object
instance and objclass
definition. Under Method 1, the corresponding elements in
object
are then updated (with updateObject(elt, ...,
verbose=verbose)
) and used as arguments to a call to new(class,
...)
, with ...
replaced by slots from the original
object. If this fails, then Method 2 tries new(class)
and
assigns slots of object
to the newly created instance.
getObjectSlots(object)
extracts the slot names and contents from
object
. This is useful when object
was created by a class
definition that is no longer current, and hence the contents of
object
cannot be determined by accessing known slots.
updateObject
returns a valid instance of object
.
updateObjectFromSlots
returns an instance of class
objclass
.
getObjectSlots
returns a list of named elements, with each
element corresponding to a slot in object
.
updateObjectTo
in the Biobase package
for updating an object to the class definition of a template (might
be useful for updating a virtual superclass).
validObject
for testing the validity of an
object.
showMethods
for displaying a summary of the
methods defined for a given generic function.
selectMethod
for getting the definition of
a specific method.
BiocGenerics for a summary of all the generics defined in the BiocGenerics package.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | updateObject
showMethods("updateObject")
selectMethod("updateObject", "ANY") # the default method
library(Biobase)
## update object, same class
data(sample.ExpressionSet)
obj <- updateObject(sample.ExpressionSet)
setClass("UpdtA", representation(x="numeric"), contains="data.frame")
setMethod("updateObject", "UpdtA",
function(object, ..., verbose=FALSE)
{
if (verbose)
message("updateObject object = 'A'")
object <- callNextMethod()
object@x <- -object@x
object
}
)
a <- new("UpdtA", x=1:10)
## See steps involved
updateObject(a)
removeMethod("updateObject", "UpdtA")
removeClass("UpdtA")
|
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
nonstandardGenericFunction for "updateObject" defined from package "BiocGenerics"
function (object, ..., verbose = FALSE)
{
if (!isTRUEorFALSE(verbose))
stop("'verbose' must be TRUE or FALSE")
result <- standardGeneric("updateObject")
check <- list(...)$check
if (is.null(check)) {
check <- TRUE
}
else if (!isTRUEorFALSE(check)) {
stop("'check' must be TRUE or FALSE")
}
if (check) {
if (verbose)
message("[updateObject] Validating the updated object ... ",
appendLF = FALSE)
validObject(result)
if (verbose)
message("OK")
}
result
}
<bytecode: 0x55ef6cf775f0>
<environment: 0x55ef6cf9fd20>
Methods may be defined for arguments: object
Use showMethods("updateObject") for currently available ones.
Function: updateObject (package BiocGenerics)
object="ANY"
object="environment"
object="envRefClass"
object="formula"
object="list"
Method Definition:
function (object, ..., verbose = FALSE)
{
if (verbose)
message("updateObject(object=\"ANY\") default for object ",
"of class '", class(object), "'")
if (length(getObjectSlots(object)) > 0L && !any(class(object) %in%
c("data.frame"))) {
updateObjectFromSlots(object, ..., verbose = verbose)
}
else {
object
}
}
<bytecode: 0x55ef6cf6aa88>
<environment: namespace:BiocGenerics>
Signatures:
object
target "ANY"
defined "ANY"
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Object of class "UpdtA"
data frame with 0 columns and 0 rows
Slot "x":
[1] -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
[1] TRUE
[1] TRUE
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.