[Bioc-devel] Documentation of GenomicRanges::follow etc. very hard to find
Hervé Pagès
hpages at fredhutch.org
Wed Feb 18 20:52:54 CET 2015
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 <hpages at fredhutch.org
> <mailto:hpages at 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.michael at gene.com <mailto: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 <mailto: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 <mailto:plijnzaad at jabber.org> ,
> philip.lijnzaad at gmail.com <mailto:philip.lijnzaad at 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>
>
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> --
> 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 <mailto:hpages at 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: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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