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

Paul Shannon pshannon at systemsbiology.org
Thu Oct 28 22:21:00 CEST 2010

I have a specific rtracklayer question, and a general S4/help question.

The specific question:  Michael helpfully suggested  the 'viewLimits' parameter to the rtracklayer track method, saying

     This is another track line parameter, called viewLimits. See class?GraphTrackLine.
     track (session, "wiggle", viewLimits = c(0, 100)) <- wiggle

Indeed, class?GraphTrackLine mentions that parameter.

But when I call this method (or what I *think* is this method), I get this:

    unused argument(s) (viewLimits = c(80, 100))

That's my specific question.   How do I supply viewLimits information to the track method?

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


and see, respectively, the parameters and the contents of the body of the function.

But with generics, args (track) gets me

   function (object, ...)

and then, looking for the definition, I do this (knowing, of course that it won't work):

  > track
    standardGeneric for "track" defined from package "rtracklayer"
    function (object, ...)
    <environment: 0x10b69b340>
    Methods may be defined for arguments: object
    Use  showMethods("track")  for currently available ones.

  > showMethods ('track')
    Function: track (package rtracklayer)

Is there something like this I should call?

   args (track (object='UCSCSession'))

Better yet -- is there a 'R help for S4 classes, objects and methods' tutorial somewhere?


 - Paul

More information about the Bioconductor mailing list