[Bioc-devel] Documentation of GenomicRanges::follow etc. very hard to find

Hi,

Philip makes a very good point. This is exactly the reason why,
a few months ago, I started to alias method man pages with the
symbol of the generic. For example I've done it for findOverlaps
and all the intra- and inter- range methods (shift, resize, flank,
range, reduce, etc...). So after loading the GenomicRanges
package, if you do ?reduce, you are presented the list of man pages
that document a "reduce" method (there is one in IRanges and one in
GenomicRanges) and you can select the one you want. If you do
?findOverlaps after loading the GenomicAlignments package, you get
to choose between 3 man pages.

I've not done this in a systematic way yet but this is the long
term plan. In the mean time, I just did it for the "precede", "follow",
"nearest", "distance", and "distanceToNearest" in GenomicRanges.
This is in GenomicRanges 1.19.38 (BioC devel). More will follow...

Cheers,
H.


On 02/18/2015 09:35 AM, James W. MacDonald wrote:

I agree with Michael. In my opinion, the help pages for S4 methods are
painfully obscure, and expecting anybody (let alone a newbie) to figure
out
that they need to do something like method?"follow,GenomicRanges,
GenomicRanges" in order to get the help page for a method is a high hurdle
indeed.

In fact, I can't remember the last time I actually tried to find a help
page for an S4 method. I much prefer traversing the methods tree using
showMethods(), and tracking down the method that will dispatch on whatever
object I have in hand, rather than trying to figure out what incredibly
unintuitive combination of names, quotes, question marks (and the required
order thereof) is required to get the help page.

Best,

Jim



On Wed, Feb 18, 2015 at 9:10 AM, Michael Lawrence <
lawrence.michael at gene.com

wrote:

 I guess this is really an argument for having _all_ method man pages be

aliased with the symbol of the generic. I wonder if R should just be made
smarter and bring up a menu whenever help is requested on a generic,
listing all of the available methods, with the default method as the
default selection.

On Wed, Feb 18, 2015 at 8:38 AM, Philip Lijnzaad <
p.lijnzaad at umcutrecht.nl

 wrote:

 On 02/18/2015 05:13 PM, Martin Morgan wrote:

 On 02/18/2015 08:05 AM, Philip Lijnzaad wrote:

     Dear all,
     looking up the documentation on functions like follow() and
precede() is
     very hard, since they are only documented under the topic
"nearest-methods",
     which currently (GenomicRanges package 1.18.4) can only be found
using the
     ?? operator (and having found the name of the topic, most newbies
are still

FWIW

 method?"follow<tab>

shows

ANY,SummarizedExperiment
GenomicRanges,GenomicRanges
GenomicRanges,missing
SummarizedExperiment,ANY
SummarizedExperiment,SummarizedExperiment
Ranges,RangesORmissing

suggesting, e.g.,

 method?"follow,GenomicRanges,GenomicRanges"

 Hi Martin, thanks for the feedback. To be honest, your solution

involves
more typing, and is not newbie-friendly since the
newbie doesn't now anything about "methods". S/he simply types ?follow

and

gets back an answer (from the IRanges docu),
and subsequently thing "oh well, follow() doesn't know about strands,
and
then gets stuck). My request is simply to add the plain \alias{}es, i.e.
just like we have for findOverlaps and the methods described in
inter-range-methods.Rd. Or what would be the argument against that?

Cheers,


Philip

--
Philip Lijnzaad, PhD
Molecular Cancer Research
University Medical Center (UMC), Utrecht
Stratenum room 2.211
IM: plijnzaad at jabber.org , philip.lijnzaad at gmail.com
P.O. Box 85060, 3508 AB Utrecht
(Universiteitsweg 100, 3584 CG Utrecht)
The Netherlands
tel: +31 (0)8875 68464

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