I get your point with the multiple inheritance example, but I did not mean to give a general work around for all inheritance situation, but rather for the specific case of the initialize method of class ExpressionSet. I understand that touching class ExpressionSet is a very sensitive matter given its central role in BioConductor, and it is already great as it is. I will definitely have a look at the IRange class to get some inspirations. Thanks. Renaud On 16/12/2010 08:46, Martin Morgan wrote: > On 12/15/2010 10:05 PM, Renaud Gaujoux wrote: >> Hi Morgan, >> >> thank you very much for the explanation on the initialize method for the >> class ExpressionSet. >> I always found the S4 initialization mechanism a bit difficult to handle >> in the case of inheritance. It often requires to manually pass slots to >> the parent class, which should be automatic: each class -- developer -- >> has to deal only with its own data members. >> >> Maybe I am too optimistic, but would something like the following >> definition of initialize,ExpressionSet-method fix the problem without >> changing the current behaviour for the dependent packages (since I >> assume they all pass assayData as a first argument): > It's really hard to get S4 right, and the constraints on class and > method definition are only weakly enforced, so people have come up with > solutions that are not really optimal. From ?initialize, we have > > ...: data to include in the new object. Named arguments > correspond to slots in the class definition. Unnamed > arguments must be objects from classes that this class > extends. > > Note the plural 'classes' and > > setClass("A", representation=representation(a="integer")) > setClass("B", representation=representation(b="numeric")) > setClass("C", contains=c("A", "B")) > >> new("C", new("A", a=1:5), new("B", b=pi)) > An object of class "C" > Slot "a": > [1] 1 2 3 4 5 > > Slot "b": > [1] 3.141593 > > so your solution (checking the first arg) isn't enough. > > I'll mention that the documentation can point to solutions that will not > work well with inheritance, e.g., from ?"initialize-methods" the two > examples > > setMethod("initialize", "traceable", > function(.Object, def, tracer, exit, at, print) ... > ) > > and > > function(.Object, x, ...) { > Object<- callNextMethod(.Object, ...) > if(!missing(x)) { # do something with x > > both use arguments that are inconsistent with the description of > ?initialize. > > Also, ExpressionSet was (re)-developed five years ago, and at least some > of the more recent classes, e.g., in IRanges, are more appropriately > implemented. > > Martin > >> structure(function (.Object, ...) >> { >> # check if the first argument is an ExpressionSet >> # if so: initialize the object with it and tells .local not to >> # overwrite slots corresponding to missing arguments. >> # otherwise: s >> overwrite.missing<- TRUE >> dotargs<- list(...) >> if( length(dotargs)> 1&& is(dotargs[[1]], 'ExpressionSet') ){ >> .Object<- dotargs[[1]] >> overwrite.missing<- FALSE >> dotargs<- dotargs[-1] >> } >> >> # .local should initialize (i.e. overwrite) a slot of .Object with >> its prototype only if overwrite.missing=TRUE, or in any case with the >> corresponding non missing argument for this slot. >> .local<- function (.Object, overwrite.missing=TRUE, assayData, >> phenoData, featureData, >> exprs = new("matrix"), ...) >> { if (overwrite.missing&& missing(assayData)) { >> # stuff ... >> } >> # other stuff ... >> } >> >> # call .local with overwrite.missing as its first argument >> do.call(.local, c(list(.Object, overwrite.missing), dotargs)) >> >> } >> >> I think this would allow: >> >> eset<- new('ExpressionSet', exprs=matrix(0,10,5)) >> new('ExpressionSet', eset) # simple copy constructor >> new('ExpressionSet', eset, exprs=matrix(0,20,3)) # overwrite original >> exprs with the one given in argument >> # etc... with other slots >> # and the current behaviour should also work >> new('ExpressionSet', assayData=assayData(eset), exprs=matrix(0,10,5)) >> # and initialize will still set the object to its prototype if directly >> called (which a behaviour one might not want to change as it could be >> use by other packages) >> initialize(eset) >> >> >> Thank you. >> Renaud >> >> >> >> >> >> On 15/12/2010 20:21, Martin Morgan wrote: >>> On 12/15/2010 09:42 AM, Renaud Gaujoux wrote: >>>> Hi, >>>> >>>> I am trying to extend class ExpressionSet in a very simple way to add an >>>> extra slot. >>>> Now suppose I have a valid ExpressionSet object, I want to create an >>>> object of class 'A' as follows (this always worked with other S4 classes >>>> I defined): >>>> >>>> library(Biobase) >>>> setClass('A', representation(extraslot='list'), >>>> contains='ExpressionSet') >>>> eset<- new('ExpressionSet') >>>> new('A', eset) >>>> >>>> # this throws the error: >>>> Error in function (classes, fdef, mtable) : >>>> unable to find an inherited method for function >>>> "annotatedDataFrameFrom", for signature "ExpressionSet" >>>> #Note: this also does not work with a non-empty ExpressionSet object. >>>> >>>> Is this normal? Is there a specific way to extend the class >>>> ExpressionSet? >>>> The classes I found that extend ExpressionSet add an extra element in >>>> assayData, and from what I saw it requires defining an initialize method >>>> to pass all the standard parameters to the underlying ExpressionSet >>>> object (exprs, phenoData, featureData, etc...) >>> Hi Renaud -- >>> >>> This is an unfortunate consequence of the 'initialize' method that your >>> class inherits from ExpressionSet. 'new' uses the prototype of 'A' to >>> create .Object, and then passes .Object and other arguments to 'new' >>> down to 'initialize'. The 'initialize' method inherited from >>> ExpressionSet is in part >>> >>>> head(selectMethod(initialize, 'A')) >>> 1 structure(function (.Object, ...) >>> 2 { >>> 3 .local<- function (.Object, assayData, phenoData, featureData, >>> 4 exprs = new("matrix"), ...) >>> 5 { >>> 6 if (missing(assayData)) { >>> >>> with .local invoked so as .local(.Object, ...) in the body of >>> initialize. So your 'eset' is the seen as the second argument, and >>> matches by position with the argument 'assayData'; this is not expected >>> to be an ExpressionSet, and trouble ensues. In retrospect the 'right' >>> signature for initialize,ExpressionSet-method would have placed the >>> named arguments after ..., with the user needing to supply named >>> assayData= etc arguments. >>> >>> An additional problem is that the initialize,ExpressionSet-method >>> assumes that .Object is from its prototype, so for instance an exprs >>> with non-zero dimensions is overwritten >>> >>>> eset<- new("ExpressionSet", exprs=matrix(0,10,5)) >>>> eset >>> ExpressionSet (storageMode: lockedEnvironment) >>> assayData: 10 features, 5 samples >>> element names: exprs >>> protocolData: none >>> phenoData: none >>> featureData: none >>> experimentData: use 'experimentData(object)' >>> Annotation: >>>> initialize(eset) >>> ExpressionSet (storageMode: lockedEnvironment) >>> assayData: 0 features, 0 samples >>> element names: exprs >>> protocolData: none >>> phenoData: none >>> featureData: none >>> experimentData: use 'experimentData(object)' >>> Annotation: >>> >>> You're stuck working with the initialize,ExpressionSet-method as defined >>> (changing it now would disrupt a lot of package and user code), probably >>> the easiest way being to write an appropriate initialize method or, >>> probably better given the pitfalls of doing this correctly, write a >>> constructor that does what you want >>> >>> library(Biobase) >>> setClass('A', representation(extraslot='list'), >>> contains='ExpressionSet', >>> prototype=prototype(extraslot=list(a=1:5))) >>> >>> setGeneric("A", function(x, ...) standardGeneric("A")) >>> setMethod(A, "missing", function(x, ...) new("A", ...)) >>> setMethod(A, "ExpressionSet", function(x, ...) { >>> new("A", assayData=assayData(x), phenoData=phenoData(x), >>> featureData=featureData(x), ...) ## protocalData here too? >>> }) >>> >>> ## test >>> eset<- new('ExpressionSet', exprs=matrix(0, 10, 5)) >>> A(eset) >>> A() >>> A(eset)@extraslot >>> A()@extraslot >>> A(eset, extraslot=list(b=5:1))@extraslot >>> A(extraslot=list(b=5:1))@extraslot >>> >>> Martin >>> >>>> Thank you for any insight on the matter. >>>> Renaud >>>> >>>> sessionInfo: >>>> R version 2.12.0 (2010-10-15) >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_ZA.utf8 LC_NUMERIC=C LC_TIME=en_ZA.utf8 >>>> LC_COLLATE=en_ZA.utf8 LC_MONETARY=C LC_MESSAGES=en_ZA.utf8 >>>> LC_PAPER=en_ZA.utf8 >>>> [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C >>>> LC_MEASUREMENT=en_ZA.utf8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] Biobase_2.8.0 >>>> >>>> >>>> >>>> >>>> ### >>>> UNIVERSITY OF CAPE TOWN >>>> This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:5}} >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> ### >> UNIVERSITY OF CAPE TOWN >> This e-mail is subject to the UCT ICT policies and e-mail disclaimer >> published on our website at >> http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from >> +27 21 650 9111. 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