Hi Musa --
Musa Parmaksiz wrote:> Hi R-Help,
>
> Please consider the following simple case: I have a class like
>
> setClass("myClass",
> representation(x="matrix",
y="character"))
>
> and I would like to use the method *"["* for a *myClass* objects
(but
> changing the default *drop* argument from TRUE to FALSE):
>
> setMethod("[","myClass",
> function(x,i,j,...,drop=FALSE)
> {
> x <- x at x
> callNextMethod()
I think you are hoping that x at x will be subsetted, and it appears that
it is. But I think this is a bug. 'callNextMethod' without any arguments
should be using the 'x' in the signature. This should result in an error
like the one seen here
setMethod("[",
signature=signature(x="myClass"),
function(x, i, j, ..., drop=FALSE)
{
callNextMethod()
})
> test[1,]
Error in x[i = i, j = , ...] : object is not subsettable
Normally, to change the value of the variable 'seen' by the next method,
one would expect to have to write something like
setMethod("[",
signature=signature(x="myClass"),
function(x, i, j, ..., drop=FALSE)
{
callNextMethod(x=x at x, i=i, j=j, ..., drop=drop)
})
You can now see how this is a little more complicated -- if j is missing
in the original function call, then it can't be used in an assignment in
callNextMethod. You'd have to write something like
setMethod("[",
signature=signature(x="myClass"),
function(x, i, j, ..., drop=FALSE)
{
if (missing(i) && missing(j))
callNextMethod(x=x at x,,, ..., drop=drop)
else if (missing(j))
callNextMethod(x=x at x, i=i, , ..., drop=drop)
else if (missing(i))
callNextMethod(x=x at x, , j=j, ..., drop=drop)
else
callNextMethod(x=x at x, i=i, j=j, ..., drop=drop)
})
or, since this is really an implementation that dispatches on the
'misssing'-ness of i, j, a series of methods like
setMethod("[",
signature=signature(
x="myClass",
i="ANY',
j="missing")
function(x, i, j, ..., drop=FALSE)
{
callNextMethod(x at x, i=i, , ..., drop=drop)
})
Notice too how it is necessary to specify the argument list in quite an
odd way, with a ',' for the 'missing' variable(s). This is
because "["
is a so-called 'Primitive' function, and primitive functions match by
position rather than the usual matching by name:
> matrix(1:20,5)[4,2]
[1] 9
> matrix(1:20,5)[j=4,i=2]
[1] 9
!
I read somewhere that when faced with learning complicated systems,
otherwise intelligent people will develop wildly inaccurate stories to
explain why the system 'works'. The above is my story.
Martin
> x<-as.myClass(x)
> }
> )
>
> suppose that *as.myClass* method has been already defined. Actually, all I
> want is to pass all the arguments to *"["* method for *matrix*,
except
> changing the default behaviour for *drop*.
>
> When I execute:
>> test<-new("myClass",x=cbind(1:3,4:6),y="a")
>> test[1,] # works as expected
> [1] 1 4
>
>> test[1,drop=TRUE] # does not work
> Error: argument "j" is missing, with no default
> Error in callNextMethod() : error in evaluating a 'primitive' next
method
>
> but with a matrix the two cases work:
>> m<-cbind(1:3,4:6)
>> m[1,]
> [1] 1 4
>> m[1,drop=TRUE]
> [1] 1
>
> Can you please advise me a solution for this problem?
> Thank you in advance for the help.
>
> Musa
>
> [[alternative HTML version deleted]]
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
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Phone: (206) 667-2793