[Bioc-devel] recalling methods

Michael Lawrence lawrence.michael at gene.com
Thu Dec 4 22:01:18 CET 2014

I think this gets at the heart of at least one of the usability issues in
Bioconductor: interface discoverability. Many simpler command line tools
have a single-faceted interface for which it is easy to enumerate a list of
features. There's definitely room for better ways to interrogate our
object-oriented APIs, but it's challenging. Essentially we need a way for
the user to ask "what can I do with this object?". Yes, we need better
introspection utilities, but we also need to integrate the query with
documentation. In other words, we need a more dynamic, more fluid help
system, oriented around S4.

On Thu, Dec 4, 2014 at 9:56 AM, Michael Love <michaelisaiahlove at gmail.com>

> I was thinking about a request from someone at Bioc2014 (I can't
> remember at the moment)
> As an end-user, if I have an object x, how can I *quickly* recall the
> main methods for that? As in, without breaking my flow and going to
> ?myClass or help("myClass-class"). Suppose x is a GRanges, how can I
> remember that there is a method called narrow() which works on x?
> showMethods(classes=class(x)) will print out a huge list for many
> complex Bioc classes. And printTo=FALSE turns this huge list into an
> unhelpful character vector, e.g.:
> head(showMethods(classes="GRanges",printTo=FALSE),8)
> [1] ""                                    "Function \".asSpace\":"
>   [3] " <not an S4 generic function>"       ""
>   [5] "Function \".linkToCachedObject<-\":" " <not an S4 generic function>"
>   [7] ""                                    "Function \".replaceSEW\":"
> any ideas?
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