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

[Michael Lawrence]

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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