[BioC] no summary of GOHyperGResult
Robert Castelo
robert.castelo at upf.edu
Fri Jul 9 17:03:38 CEST 2010
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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