Dear Wolfgang
Thank you very much for pointing me to this link, in principle this
would answer my question: Method updateObject() of package Biobase would
be exactly what I am looking for. However, I have hoped that maybe there
is also a solution for S4 classes in general.
Somehow I feel that package Biobase has solved a couple of shortcomings
of S4 classes. People may not agree with me but I think that method
"updateObject()" should belong to package "methods" so that every S4
class can profit from it.
Nevertheless, thank you once again, I will have a look at the code of
package Biobase.
Best regards and Happy New Year
Christian
Wolfgang Huber wrote:
Dear Christian
this post from Martin Morgan on class versioning in Bioconductor's
Biobase package might be relevant:
https://stat.ethz.ch/pipermail/bioc-devel/2006-May/000545.html
and also section 6 of this:
http://www.bioconductor.org/packages/2.4/bioc/vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf
Best wishes
Wolfgang
Wolfgang Huber EMBL-EBI http://www.ebi.ac.uk/huber
cstrato wrote:
Dear all,
Since my package is based on S4 classes, I would like to know how to
add a slot to an existing S4 class without breaking the code of users
of my package.
Assume the following S4 class:
setClass("MyClass",
representation(name = "character",
type = "character",
data = "data.frame"
),
prototype(name = "",
type = "Default",
data = data.frame(matrix(nr=0,nc=0))
)
)#MyClass
Assume that a user has created an object:
> myclass <- new("MyClass", name="MyName", type="MyType", data=tmp)
> str(myclass)
Now I would like to add another slot "info" to MyClass:
setClass("MyClass",
representation(name = "character",
type = "character",
data = "data.frame",
info = "data.frame"
),
prototype(name = "",
type = "Default",
data = data.frame(matrix(nr=0,nc=0)),
info = data.frame(matrix(nr=0,nc=0))
)
)#MyClass
Now when the user loads my package with S4 class MyClass containing a
new slot and calls:
> str(myclass)
Error in FUN(c("name", "type", "data", "info")[[4L]], ...) :
no slot of name "info" for this object of class "MyClass"
>
My question is:
Is there any possibility or special trick, which would avoid this
error message?
Are there other possibilities to access an additional data.frame from
an existing class?
Is there something like an "evolution" of S4 classes, which
distinguishes the different implementations of an S4 class, and
allows the user to keep the object of an old class?
Best regards
Christian
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V.i.e.n.n.a A.u.s.t.r.i.a
e.m.a.i.l:cstrato at aon.at
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