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

[Martin Morgan]

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"

>     lost  since  ?nearest-methods  lands you in the man page on Arithmetic
>     Operators, since they didn't do ?`nearest-methods`)
>     I see that the nearest-methods.Rd file contains aliases such as
>     \alias{follow,GenomicRanges,GenomicRanges-method}
>     \alias{follow,GenomicRanges,missing-method}
>     but   methods   from   many  other  Bioconductor  packages,  including
>     IRanges::findOverlaps   and   GenomicRanges::findOverlaps  have  plain
>     unqualified  \alias{methodname} lines in their man pages as well, which
>     makes it much easier to look up documentation. (Of course, the user may be
>     presented with the "Help on topic such-and-such was found in the following
>     packages:"-dialogue but that is fine).
>     So my question is: is there a good reason not to add the following general
>     aliases
> \alias{precede)
> \alias{follow)
> \alias{nearest)
> \alias{distance)
> \alias{distanceToNearest)
>
>     in nearest-methods.Rd ?Without them, it's hard to look up the documentation,
>     so   can  these  general  aliases  please  be  added,  just  like  for
>     inter-range-methods.Rd? Many thanks in advance,
>     Philip
>
>     --
>     Philip Lijnzaad, PhD
>     Molecular Cancer Research
>     University Medical Center (UMC), Utrecht
>     Stratenum room 2.211
>     IM: [1]plijnzaad at jabber.org , [2]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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>
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