R help - Oct 2009 - How to get the definition of a class?

Hi,

ExonFeatureSet

I have an object of the above class. The following document mentioned it.

http://www.bioconductor.org/packages/2.5/bioc/vignettes/oligo/inst/doc/ClassesUsedInOligo.pdf

But I would like to see its defintion. I'm wondering if there is a way
in R to give me the definition of any class?

Regards,
Peng

Peng Yu wrote:
> Hi,
> 
> ExonFeatureSet
> 
> I have an object of the above class. The following document mentioned it.
> 
>
http://www.bioconductor.org/packages/2.5/bioc/vignettes/oligo/inst/doc/ClassesUsedInOligo.pdf
> 
> But I would like to see its defintion. I'm wondering if there is a way
> in R to give me the definition of any class?
It is defined by a call to setClass in the package that defines it
(oligoClasses); I believe the package source (in this case,
oligoClasses/R/AllClasses.R) is the only place where the explicit call
is available.

A representation of the class is available with

  cls = getClass("ExonFeatuereSet")

show(cls) displays a summary of the class, class(cls) tells you how
classes are represented (as class classRepresentation),
class?classRepresentation provides information on the representation of
classes.

oligoClasses:::.__C__ExonFeatureSet is the definitive instance of the
class representation (hiding inside the name space and obscured, so
clearly not meant for direct access).

Martin
> 
> Regards,
> Peng
> 
> ______________________________________________
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

On Tue, Oct 13, 2009 at 9:38 PM, Martin Morgan <mtmorgan at fhcrc.org>
wrote:
> Peng Yu wrote:
>> Hi,
>>
>> ExonFeatureSet
>>
>> I have an object of the above class. The following document mentioned
it.
>>
>>
http://www.bioconductor.org/packages/2.5/bioc/vignettes/oligo/inst/doc/ClassesUsedInOligo.pdf
>>
>> But I would like to see its defintion. I'm wondering if there is a
way
>> in R to give me the definition of any class?
>
> It is defined by a call to setClass in the package that defines it
> (oligoClasses); I believe the package source (in this case,
> oligoClasses/R/AllClasses.R) is the only place where the explicit call
> is available.
>
> A representation of the class is available with
>
> ?cls = getClass("ExonFeatuereSet")
>
> show(cls) displays a summary of the class, class(cls) tells you how
> classes are represented (as class classRepresentation),
> class?classRepresentation provides information on the representation of
> classes.
>
> oligoClasses:::.__C__ExonFeatureSet is the definitive instance of the
> class representation (hiding inside the name space and obscured, so
> clearly not meant for direct access).
Are functions like slotNames, show, etc., that are mentioned in
Section C (Memo) of the Appendix in "A (Not So) Short Introduction to
S4" defined in R language? Or they are function that should be provide
by any S4 class?