Mike,
This makes sense (I was actually surprised I was able to get my example to
work as easily as I did).
The thing is, if you are dispatching on i (which you must if any methods
do), you HAVE to know what class i is in order to identify the method.
AFAIK there is no way in R of doing that without evaluating the object.
So I guess we're back to "no, you can't do that".
Sorry for the noise and for getting your hopes up. You can always write a
subset S3 method.
~G
On Wed, Aug 6, 2014 at 1:45 PM, Mike <wjia...@fhcrc.org> wrote:
> Gebe,
>
> Your suggestion only works in an environment where no formal argument 'i'
> is defined in any of existing '[' method. e..g
>
>
> > showMethods("[")
> Function: [ (package base)
> x="nonStructure"
>
> Once we load the package that exports '[' methods with 'i' (e.g.
> 'flowCore' ), then method dispatch still tries to evaluate 'i' in order to
> match the call to the available methods.
>
> > library(flowCore)
>
> > showMethods("[")
> Function: [ (package base)
> x="AnnotatedDataFrame", i="ANY"
> x="container", i="ANY"
> x="eSet", i="ANY"
> x="filterResultList", i="ANY"
> x="filterSet", i="character"
>
> x="flowFrame", i="ANY"
> ...
>
> > y[holycrapnothere]
>
> Error: object 'holycrapnothere' not found
>
>
> Mike
>
> On 08/06/2014 11:45 AM, Gabe Becker wrote:
>
> Mike,
>
> This can be done. I would argue that the convenience your users get from
> this is far outweighed by the damage this does to the ability to read and
> easily understand the code they are writing. Users, maintainers, etc now
> need to know the object class, what columns it has and what variables are
> in their environment in order to predict a '[' expression's behavior.
> (This is why most people I know to won't touch the attach function with a
> 10 foot pole, regardless of how convenient it seems at first).
>
> But anyway, I'm not the design police and my dislike of non-standard
> evaluation is far from universal, so here is how to do it:
>
> > setClass("toydf", representation(x = "data.frame"))
> > setMethod("[", "toydf", function(x, i, j, ...) {key = substitute(i) ;
> eval(key, x@x, parent.frame())})
> [1] "["
> > x = data.frame(holycrapnothere = 1:6)
> > y = new("toydf", x= x)
> > y
> An object of class "toydf"
> Slot "x":
> holycrapnothere
> 1 1
> 2 2
> 3 3
> 4 4
> 5 5
> 6 6
>
> > holycrapnothere
> Error: object 'holycrapnothere' not found
> No suitable frames for recover()
>
> > y[holycrapnothere]
> [1] 1 2 3 4 5 6
>
>
> ~G
>
>
>
> On Wed, Aug 6, 2014 at 10:43 AM, Mike <wjia...@fhcrc.org> wrote:
>
>> I'd like to do 'data.table-like' subsetting on `S4 class` by using 'i
>> expression'. However, '[' generic function has the problem to dispatch S4
>> method because of its early evaluation of i argument.
>> e.g.
>>
>> > gslist[Visit == 1, ]
>> Error in gslist[Visit == 1, ] :
>> error in evaluating the argument 'i' in selecting a method for function
>> '[': Error: object 'Visit' not found
>>
>> Here 'gslist' is a S4 object `GatingSet` .
>>
>> I wasn't able to bypass this even after I defined my own S3 method (e.g
>> [.GatingSet).
>> I guess it is because 'GatingSet' is S4 class and there are already some
>> S4 methods defined by other packages
>>
>> > showMethods("[")
>> Function: [ (package base)
>> x="AnnotatedDataFrame", i="ANY"
>> x="flowFrame", i="ANY"
>> ...
>>
>> So it will always try these S4 methods before any S3 gets its chance.
>>
>> Is there better way other than these two?
>> 1. change 'GatingSet' to S3 class
>> 2. use a different generic function that is not associated with any S4
>> methods (e.g. subset)
>>
>> Mike
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> Computational Biologist
> Genentech Research
>
>
>
--
Computational Biologist
Genentech Research
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