Hi Michael, On 02/18/2015 11:12 AM, Michael Lawrence 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.
If the proposal is to have R bring up a menu listing all of the available methods, then the user will have to choose amongst 30+ methods every time s/he does ?length or ?findOverlaps. I think this is probably overwhelming for most newbies. It's also confusing to have so many entries to choose amongst when they are only taking you to 2 or 3 different man pages. So I'd rather stick to a menu listing the man pages rather than the methods. Don't know how hard it would be to have R do this automatically though... Thanks, H.
On Wed, Feb 18, 2015 at 10:50 AM, Hervé Pagès <hpa...@fredhutch.org <mailto: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 <mailto: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 <mailto: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 <mailto:plijnz...@jabber.org> , philip.lijnz...@gmail.com <mailto:philip.lijnz...@gmail.com> P.O. Box 85060, 3508 AB Utrecht (Universiteitsweg 100, 3584 CG Utrecht) The Netherlands tel: +31 (0)8875 68464 <tel:%2B31%20%280%298875%2068464> ------------------------------__------------------------------ ------------------ 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 <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <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 <mailto:hpa...@fredhutch.org> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
-- 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
