On Thu, Dec 4, 2014 at 4:01 PM, Michael Lawrence <lawrence.mich...@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 <michaelisaiahl...@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@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel