What Michael suggests is obviously the way forward. To be clear: what Herve is doing is somewhat simple though: if a man page is for a specific method, it should also contain \alias{$GENERIC}
Kasper On Wed, Feb 18, 2015 at 2:12 PM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > Great. I was just wondering whether we could make the job of the developer > easier by having R find the methods, instead of needing to add aliases to > every method man page. > > On Wed, Feb 18, 2015 at 10:50 AM, Hervé Pagès <hpa...@fredhutch.org> > wrote: > > > 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.mich...@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.lijnz...@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: plijnz...@jabber.org , philip.lijnz...@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@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: hpa...@fredhutch.org > > Phone: (206) 667-5791 > > Fax: (206) 667-1319 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel