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
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
