[BioC] On extending class ExpressionSet

Renaud Gaujoux renaud at mancala.cbio.uct.ac.za
Thu Dec 16 08:01:42 CET 2010


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. This e-mail is intended only for the person(s) to whom
>> it is addressed. If the e-mail has reached you in error, please notify
>> the author. If you are not the intended recipient of the e-mail you may
>> not use, disclose, copy, redirect or print the content. If this e-mail
>> is not related to the business of UCT it is sent by the sender in the
>> sender's individual capacity.
>>
>> ###
>>
>>
>

 

###
UNIVERSITY OF CAPE TOWN 

This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:5}}



More information about the Bioconductor mailing list