[Bioc-devel] Documentation of GenomicRanges::follow etc. very hard to find
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
_________________________________________________________________
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 is...{{dropped:14}}
References
1. mailto:plijnzaad at jabber.org
2. mailto:philip.lijnzaad at gmail.com
_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793