[R] Methods to explore R data structures

[Martin Morgan]

On 05/27/2010 02:13 AM, Timothy Wu wrote:
> Hi,
>
> I'm very confused about R structures and the methods to go with them.
> I'm using R for microarray analysis with Bioconductors. Suppose
> without reading the documentations, what's the best way to explore a
> data structure when you know nothing about it?

probably by reading the documentation, especially vignettes

 > browseVignettes("Biobase")

and then switching to your web browser. If you're asking about
Bioconductor functionality in particular, then the Bioconductor mailing
list is appropriate

  http://bioconductor.org/docs/mailList.html

>
> I am currently using is() / class() to see what the object is. str()
> / attributes() to probe inside the object, and
> something at something$something to walk it and explore. Is there any

This looks at the structure, but many classes will want to be
manipulated by their API.

> other way? . Also, without reading documentations, is there a way to
> know what functions are available to extract data from it? For
> example, there is sampleNames() which works on ExpressionSet and
> AnnotatedDataFrame (which is a part of ExpressionSet). How do I know
> they are available (as sometimes I can't recall where I've seen them
> and I forgot the function names). And what are R functions? Are
> those

For an S4 object 'x', I'd

  class(x)
  getClass(cls)@package

followed by

  showMethods(classes='ExpressionSet',
              where=getNamespace('Biobase'))

or

  cls <- c(class(x), getClass(class(x))@contains)
  pkg <- getClass(cls)@package
  showMethods(classes=cls, where=getNamespace(pkg))

and conversely

  showMethods(sampleNames, where=getNamespace(pkg))

Methods for S3 classes can be found in a similar way, but using
'methods'. Both of these only discover classes in packages that are
loaded in the currently active session. This will miss plain old
functions that don't declare what type of object they intend to operate
on. If whan you say 'what are the R functions' you're asking for the
function definition, then

  selectMethod(sampleNames, 'ExpressionSet')

> two separate functions or polymorphic functions? I'm also pretty

sampleNames is a generic. There are methods that operate on eSet (a base
class of ExpressionSet), and on AnnotatedDataFrame.

> confused about S3, S4, or the regular list. I guess I'm fairly
> confused about R in general.

For S4

  ?Methods
  ?Classes

For S3, maybe section 10.9 of RShowDoc('R-intro')

Martin

>
> Any good source of reading (hopefully short and understandable, too)
> would be appreciated. Thanks.
>
> Timothy
>
> [[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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