[BioC] no summary of GOHyperGResult

[Martin Morgan]

On 07/08/2010 01:56 PM, Robert M. Flight wrote:
> This strikes me as really weird (and annoying) behavior.
> 
> I have a GOHyperGResult, calculated using GOstats and Category from
> which I want to obtain a summary. This summary call is within a
> function, that I tested time and time again to verify that it was
> working (worked yesterday, haven't changed my setup). However, now,
> whenever I call summary on the GOHyperGResult in my function, I get
> this (via browser(expr=TRUE) just before where I would actually use
> it):
> 
> R> summary(GOHyperGResultObject)
> 
>        Length          Class           Mode
>              1 GOHyperGResult             S4
> 			
> However, showMethods("summary") gives the following:
> 
> Function: summary (package base)
> object="AnnDbBimap"
> object="ANY"
> object="Bimap"
> object="DBIObject"
> object="GOHyperGResult"
> object="HyperGResultBase"
> object="KEGGHyperGResult"
> object="LinearMResultBase"
> object="PFAMHyperGResult"
> object="SQLiteConnection"
> object="SQLiteDriver"
> object="SQLiteResult"
> 
> When outside the function (in the base workspace), I get the actual
> summary I am after. However, when I check if there is a difference in
> showMethods("summary"), I see the same list:
> Function: summary (package base)
> object="AnnDbBimap"
> object="ANY"
> object="Bimap"
> object="DBIObject"
> object="GOHyperGResult"
> object="HyperGResultBase"
> object="KEGGHyperGResult"
> object="LinearMResultBase"
> object="PFAMHyperGResult"
> object="SQLiteConnection"
> object="SQLiteDriver"
> object="SQLiteResult"
> 
> The object in the base workspace is a save of the object being
> generated in my function, so I know it is not because they are
> different objects. I thought this might due to installing a new
> package (KEGGgraph was the last one I installed), but even after
> removing and restarting the same behavior continues.
> 
> If anyone could shed some light on this behavior, I would really,
> really appreciate it, because I can't see why this is happening. My
> function is in a package, do I need to explicitly import the "summary"
> method from GOstats in the NAMESPACE? I already have GOstats in the
> require, and it loads the package.

If your function is in a package, then yes, you should in the
DESCRIPTION file

  Imports: GOstats

and

  importClassesFrom(GOstats, GOHyperGResult)
  importMethodsFrom(GOstats, summary)

It sounds like your package has code

  require(GOstats)

but that's not what you want to do -- it'll attach GOstats to the search
path, but you want GOstats, or at least the summary methods defined in
GOstats, available to your package without relying on the structure of
the (user modifiable) search path.

I don't know the details behind Jim's suggestion, but a certain amount
of water has passed under the bridge since then and I'd be interested in
knowing whether those contortions are actually necessary in an
appropriately structured package.

Martin


> 
> Cheers,
> 
> -Robert
> 
> R version 2.11.1 (2010-05-31)
> i386-pc-mingw32
> 
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
>  [1] org.Mm.eg.db_2.4.1    GO.db_2.4.1           categoryCompare_0.1-1
>  [4] biocGraph_1.10.0      Rgraphviz_1.26.0      hwriter_1.2
>  [7] GOstats_2.14.0        RSQLite_0.9-1         DBI_0.2-5
> [10] graph_1.26.0          Category_2.14.0       AnnotationDbi_1.10.1
> [13] Biobase_2.8.0
> 
> loaded via a namespace (and not attached):
>  [1] annotate_1.26.0    genefilter_1.30.0  geneplotter_1.26.0 GSEABase_1.10.0
>  [5] RBGL_1.24.0        RColorBrewer_1.0-2 splines_2.11.1     survival_2.35-8
>  [9] tools_2.11.1       XML_3.1-0          xtable_1.5-6
> 
> Robert M. Flight, Ph.D.
> Bioinformatics and Biomedical Computing Laboratory
> University of Louisville
> Louisville, KY
> 
> PH 502-852-0467
> EM robert.flight at louisville.edu
> EM rflight79 at gmail.com
> 
> Williams and Holland's Law:
>        If enough data is collected, anything may be proven by
> statistical methods.
> 
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-- 
Martin Morgan
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