[BioC] no summary of GOHyperGResult

Robert M. Flight rflight79 at gmail.com
Thu Jul 8 22:56:55 CEST 2010


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.

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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