[Bioc-devel] recalling methods

I just noticed in the newsletter [1] that Martin fixed this in R-devel / R
3.2

methods(class="GenomicRanges")

  [1] !=                [                 [<-               %in%
   <
...

thanks Martin!

[1]
http://www.bioconductor.org/help/newsletters/2015_April/#new-and-noteworthy

On Sat, Dec 6, 2014 at 5:32 PM, Michael Lawrence <lawrence.michael at gene.com>
wrote:

On Sat, Dec 6, 2014 at 9:23 AM, Wolfgang Huber <whuber at embl.de> wrote:

Also some interest on our side to contribute.
Perhaps in particular the rendering a useful index (or graph) of man
pages on the fly in HTML / graphically.

Great, that's the sort of thing I had in mind.

Is it too ambitious to ?learn? which methods are most important for
objects of a particular class from analysing (running) a large code base
(or even injecting a hook to that effect into a user?s R)?

It's a good idea and one that Eclipse and other IDEs use for
auto-completion. We'd just have to find the right codebase, i.e., something
with a lot of end-user analysis code, instead of infrastructure.

Wolfgang

On Dec 6, 2014, at 1:19 GMT+1, Michael Love <

michaelisaiahlove at gmail.com> wrote:

nice. I will play around with this. thanks Gabe!

On Fri, Dec 5, 2014 at 6:37 PM, Gabe Becker <becker.gabe at gene.com>

wrote:

Hey guys,

Surgically removed from promptClass:

 classInSig <- function(g, where, cl) {
       cl %in% unique(unlist(findMethods(g, where)@signatures))
   }
   genWithClass <- function(cl, where) {
       allgen <- getGenerics(where = where)
       ok <- as.logical(unlist(lapply(allgen, classInSig, cl = cl,
           where = where)))
       allgen[ok]
   }

genWithClass("IRanges", find(classMetaName("IRanges")))

[1] "c"            "coerce"       "end<-"        "gaps"

 "intersect"

[6] "isNormal"     "names<-"      "names"        "pgap"
"pintersect"
[11] "psetdiff"     "punion"       "reduce"       "reverse"

"setdiff"

[16] "start<-"      "start"        "threebands"   "union"
"updateObject"
[21] "update"       "width<-"      "width"


For semantic guessing of which ones will be useful, I've got nothing

(for

now).

~G

On Fri, Dec 5, 2014 at 11:28 AM, Michael Lawrence
<lawrence.michael at gene.com> wrote:

Cool. I see hypertext as being useful here, because the generics and
classes form an intricate and sometimes ambiguous web, especially when
multiple inheritance and dispatch are involved. I think we should

first

build better tooling for introspecting S4 and for graph-based

modeling and

analysis of S4 architecture. For example, could we statically detect
whether a dispatch ambiguity exists, knowing all of the methods and
classes? And based on that build one or more end-user UIs?



On Fri, Dec 5, 2014 at 11:05 AM, Michael Love
<michaelisaiahlove at gmail.com>
wrote:

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?

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--
Computational Biologist
Genentech Research

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