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

Hervé Pagès hpages at fredhutch.org
Wed Feb 18 19:50:04 CET 2015


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...


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
>>> ------------------------------------------------------------
>>> ------------------
>>> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
>>> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
>>> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender
>>> direct
>>> te informeren door het bericht te retourneren. Het Universitair Medisch
>>> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de
>>> W.H.W.
>>> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat
>> geregistreerd
>>> bij
>>> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
>>> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
>>> ------------------------------------------------------------
>>> ------------------
>>> This message may contain confidential information and ...{{dropped:11}}
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioc-devel mailing list