[BioC] On extending class ExpressionSet

[Martin Morgan]

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
> 
> 
> 
> 
> ###
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