[BioC] rtracklayer 'track' method, a viewLimits parameter?

Vincent Carey stvjc at channing.harvard.edu
Thu Oct 28 22:36:28 CEST 2010

On Thu, Oct 28, 2010 at 4:21 PM, Paul Shannon
<pshannon at systemsbiology.org> wrote:


> The general question is:  how do I navigate the help system, with S4 objects and methods, so I can figure this stuff out for myself?
> With R functions, I can type
>   args (track)
> or simply
>   track
> and see, respectively, the parameters and the contents of the body of the function.
> But with generics, args (track) gets me
>   function (object, ...)
>   NULL

getMethod("track", [signature])

will get a view of the source for the method you are interested in, and


will get them all -- can be a long dump depending on how many signatures are

>   args (track (object='UCSCSession'))
> Better yet -- is there a 'R help for S4 classes, objects and methods' tutorial somewhere?

I think it is pretty well-recognized that the many possible ways of
documenting R classes
and methods make resource discovery and use somewhat challenging.

help.search("track", agrep=FALSE)

returns useful information on my installation

in the late 1990s i wrote a javadoc-like class/method crawler for
Splus, when S4 started
to be introduced through the green book.  an example of the output is at


i have often wondered whether such a thing should be dusted off for
use with R.  there
are probably relevant developments in the roxygen area and
elsewhere... but no magic
bullet, i suspect -- the real challenge is to keep the doc current at
a fine-grained level with
evolving code structures ... not easy with such limited resources

> Thanks!
>  - Paul
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