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]plijnz...@jabber.org , [2]philip.lijnz...@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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References
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2. mailto:philip.lijnz...@gmail.com
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