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
> <mailto: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 <mailto:Bioc-devel@r-project.org> mailing
> list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
>
> --
> Computational Biologist
> Genentech Research
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