[BioC] no summary of GOHyperGResult
Robert M. Flight
rflight79 at gmail.com
Fri Jul 9 17:44:03 CEST 2010
That appears to have fixed it Robert, thank you. Now on to the next
error (isn't debugging fun)!
-Robert
On Fri, Jul 9, 2010 at 11:03, Robert Castelo <robert.castelo at upf.edu> wrote:
> hi Robert,
>
> could you try to add:
>
> summary <- getGeneric("summary")
>
> right before you make the summary call to the GOHyperGResult in your
> function?
>
> your problem sounds similar to one i found earlier this year and for
> which Seth Falcon found this workaround, you can take a look at the
> thread here:
>
> https://stat.ethz.ch/pipermail/bioconductor/2010-January/031211.html
>
>
> cheers,
> robert.
>
>
> On Fri, 2010-07-09 at 10:36 -0400, Robert M. Flight wrote:
>> Thanks to both Martin and James for the suggestions, but I give up.
>> I've tried adding the stuff to the NAMESPACE file that Martin
>> suggested, and that doesn't seem to work. However, I can't figure out
>> where or how I would add the kluge that James suggests, as this isn't
>> required in GOstats and it figures it out fine.
>>
>> I know I can access what I need using the slots of the object, I just
>> figured that I would use the methods already available.
>>
>> For the record, determining how to go from a simple function with
>> "require" to a package that has access to the right functions and
>> methods is a real pain, and the documentation is none too stupendous
>> on how to do that.
>>
>> Thanks,
>
>> -Robert
>>
>> 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.
>>
>>
>>
>> On Thu, Jul 8, 2010 at 18:42, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> > 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.
>> >>
>> >> _______________________________________________
>> >> Bioconductor mailing list
>> >> Bioconductor at stat.math.ethz.ch
>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> >
>> > --
>> > 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
>> >
>>
>> _______________________________________________
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>>
>
>
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