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## ----echo=FALSE, message=FALSE------------------------------------------------
library(Biobase)
## -----------------------------------------------------------------------------
getClass("eSet")
## -----------------------------------------------------------------------------
getValidity(getClass("eSet"))
## ----eval=FALSE---------------------------------------------------------------
# obj <- new("ExpressionSet",
# phenoData = new("AnnotatedDataFrame"),
# experimentData = new("MIAME"), annotation = character(),
# exprs = new("matrix"))
## ----eval=FALSE---------------------------------------------------------------
# assayDataNew("environment", elt)
## ----warning=FALSE------------------------------------------------------------
data(sample.ExpressionSet)
storageMode(sample.ExpressionSet)
tryCatch(assayData(sample.ExpressionSet)$exprs <- log(exprs(sample.ExpressionSet)),
error=function(err) cat(conditionMessage(err)))
## ----eval=FALSE---------------------------------------------------------------
# exprs(sample.ExpressionSet) <- log(exprs(sample.ExpressionSet))`
## -----------------------------------------------------------------------------
getClass("ExpressionSet")
getValidity(getClass("ExpressionSet"))
## -----------------------------------------------------------------------------
setClass("SwirlSet", contains="eSet")
## ----message=FALSE------------------------------------------------------------
setMethod("initialize", "SwirlSet",
function(.Object,
R = new("matrix"),
G = new("matrix"),
Rb = new("matrix"),
Gb = new("matrix"),
...) {
callNextMethod(.Object,
R=R, G=G, Rb=Rb, Gb=Gb,
...)
})
## -----------------------------------------------------------------------------
setMethod("initialize", "SwirlSet",
function(.Object,
assayData=assayDataNew(
R=R, G=G, Rb=Rb, Gb=Gb),
R = new("matrix"),
G = new("matrix"),
Rb = new("matrix"),
Gb = new("matrix"),
...) {
if (!missing(assayData) &&
any(!missing(R), !missing(G), !missing(Rb), !missing(Gb))) {
warning("using 'assayData'; ignoring 'R', 'G', 'Rb', 'Gb'")
}
callNextMethod(.Object, assayData=assayData, ...)
})
## ----eval=FALSE---------------------------------------------------------------
# new("SwirlSet")
## ----eval=FALSE---------------------------------------------------------------
# setMethod("initialize", "MySet",
# function(.Object, ...) {
# .Object <- callNextMethod(.Object, ...)
# })
## -----------------------------------------------------------------------------
setValidity("SwirlSet", function(object) {
assayDataValidMembers(assayData(object), c("R", "G", "Rb", "Gb"))
})
## ----eval=FALSE---------------------------------------------------------------
# myFancyFunction <- function(obj) {
# assayData(obj) <- fancyAssaydData # obj invalid...
# phenoData(obj) <- justAsFancyPhenoData # but now valid
# validObject(obj)
# (obj)
# }
## -----------------------------------------------------------------------------
data(sample.ExpressionSet)
classVersion(sample.ExpressionSet)
obj <- updateObject(sample.ExpressionSet)
## -----------------------------------------------------------------------------
isCurrent(sample.ExpressionSet)[c("eSet", "ExpressionSet")]
## -----------------------------------------------------------------------------
setClass("MySet",
contains = "eSet",
prototype = prototype(new("VersionedBiobase",
versions=c(classVersion("eSet"), MySet="1.0.0"))))
obj <- new("MySet")
classVersion(obj)
## -----------------------------------------------------------------------------
setClass("MySet",
contains = "eSet",
prototype = prototype(
new("VersionedBiobase",
versions=c(classVersion("eSet"), MySet="1.0.1"))))
isCurrent(obj)
## -----------------------------------------------------------------------------
setMethod("updateObject", signature(object="MySet"),
function(object, ..., verbose=FALSE) {
if (verbose) message("updateObject(object = 'MySet')")
object <- callNextMethod()
if (isCurrent(object) ["MySet"]) return(object)
## Create an updated instance.
if (!isVersioned(object))
## Radical surgery – create a new, up-to-date instance
new("MySet",
assayData = updateObject(assayData(object),
..., verbose=verbose),
phenoData = updateObject(phenoData(object),
..., verbose=verbose),
experimentData = updateObject(experimentData(object),
..., verbose=verbose),
annotation = updateObject(annotation(object),
..., verbose=verbose))
else {
## Make minor changes, and update version by consulting class definition
classVersion(object)["MySet"]<-
classVersion("MySet")["MySet"]
object
}
})
## -----------------------------------------------------------------------------
classVersion(updateObject(obj))
## -----------------------------------------------------------------------------
classVersion(new("AnnotatedDataFrame"))
## -----------------------------------------------------------------------------
setClass("SwirlSet", contains = "eSet",
prototype = prototype(
new("VersionedBiobase",
versions=c(classVersion("eSet"), SwirlSet="1.0.0"))))
classVersion(new("SwirlSet"))
## -----------------------------------------------------------------------------
obj <- new("SwirlSet")
classVersion(obj)["MyID"] <- "0.0.1"
classVersion(obj)
## -----------------------------------------------------------------------------
classVersion(updateObject(obj))
## -----------------------------------------------------------------------------
sessionInfo()
|
