[Bioc-devel] eSet extension

[Martin Morgan]

On 07/18/2011 01:34 PM, Kasper Daniel Hansen wrote:
> I am interested in extending the eSet class.  Specifically I want to
> have a number of specifically name elements in my assayData slot (I
> also have additional slots, but leave that aside).  It looks like a
> way to achieve this is by
>
> setClass("RGChannelSet",
>           contains = "eSet",
>           validity = function(object) {
>               ## msg<- validMsg(NULL,
> Biobase:::isValidVersion0(object, "RGChannelSet"))
>               msg<- validMsg(NULL,
> assayDataValidMembers(assayData(object),
>                                                          c("Red",
> "Green")))
>               if (is.null(msg)) TRUE else msg
>           })
>
> (this is clearly a two color array).  However, this fails in the sense that
>
> new("RGChannelSet")
>
> fails, presumably because nothings tells initialize that these two
> elements of assayData needs to be there.  Looking at the code for
> ExpressionSet and NChannelset, it seems like the way around this is to
> write a big initialize method that takes care of this.  I have done
> so, essentially copying most of the code from intialize-eSet, but this
> seems like code duplication.  Is there any other approach?

I'm a little rusty on ExpressionSet. I would have thought that providing 
a prototype would help, but apparently not. So I ended up with

setClass("RGChannelSet", contains = "eSet")

setValidity("RGChannelSet", function(object) {
     msg <- validMsg(NULL,
                     assayDataValidMembers(assayData(object),
                                           c("Red", "Green")))
     if (is.null(msg)) TRUE else msg
})

setMethod(initialize, "RGChannelSet",
           function(.Object, ...,
                    assayData=assayDataNew(Red=matrix(), Green=matrix()))
{
     callNextMethod(.Object, ..., assayData=assayData)
})

ExpressionSet has some unusual wrinkles. Also, it might make sense to 
extend NChannelSet instead of eSet.

Martin

>
> Now, one may ask, why do I care, because even if new("RGChannelSet")
> does not work, stuff like
>    new("RGChannelSet", Red = SOMETHING, Green = SOMETHING)
> still works.  However, it is impossible to further extend my
> RGChannelSet without errors, ie., something like
>    setClass("RGChannelExt", contains = "RGChannelSet")
> fails.
>
> Kasper
>
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