[Bioc-devel] recalling methods

Michael Love michaelisaiahlove at gmail.com
Fri Dec 5 20:05:25 CET 2014

On Thu, Dec 4, 2014 at 4:01 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> 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.

I would be interested in working on this. A minimal goal for me is a
function that just returns a character vector of the names of the
generics defined for the object. Filtering that down to give methods
which are "likely relevant" using the documentation will definitely be
a bigger challenge.

> On Thu, Dec 4, 2014 at 9:56 AM, Michael Love <michaelisaiahlove at gmail.com> wrote:
>> 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?
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list