Ah. I assumed that because I was able to generate the object I had all the
software necessary to summarize it.

Counter-intuitive but my mistake.

Thanks for the quick response,
~G


On Thu, Apr 24, 2014 at 6:58 AM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Gabe,
>
> The getAnnMap function doesn't care if the annotation package is an old
> style env or a db. In other words, the error you see is because you don't
> have KEGG.db installed, not because of a bug in the annotation package:
>
> > annotate:::getAnnMap("PATHID2NAME", "KEGG", load = TRUE)
>
> KEGG.db contains mappings based on older data because the original
>   resource was removed from the the public domain before the most
>   recent update was produced. This package should now be considered
>   deprecated and future versions of Bioconductor may not have it
>   available.  Users who want more current data are encouraged to look
>   at the KEGGREST or reactome.db packages
>
> PATHID2NAME map for KEGG (object of class "AnnDbBimap")
>
> > sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets methods
> [8] base
>
> other attached packages:
>  [1] KEGG.db_2.14.0       Category_2.30.0      GO.db_2.14.0
>  [4] RSQLite_0.11.4       DBI_0.2-7            Matrix_1.1-3
>  [7] AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2   Biobase_2.24.0
> [10] BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.42.0   genefilter_1.46.0 graph_1.42.0 grid_3.1.0
>  [5] GSEABase_1.26.0   IRanges_1.22.3    lattice_0.20-29 RBGL_1.40.0
>  [9] splines_3.1.0     stats4_3.1.0      survival_2.37-7 tools_3.1.0
> [13] XML_3.98-1.1      xtable_1.7-3
>
> Best,
>
> Jim
>
>
>
>
> On 4/24/2014 9:45 AM, Gabe Becker wrote:
>
>> Hey all,
>>
>> Apologies if I missed something. I am trying to fix a bug a user
>> identified
>> in ReportingTools, so the original code is not my own.
>>
>> It seems that the summary() method for class KEGGHyperGResult has an error
>> in it:
>>
>>  class(keggResults)
>>>
>> [1] "KEGGHyperGResult"
>> attr(,"package")
>> [1] "Category"
>>
>>> summary(keggResults)
>>>
>> Error: getAnnMap: package KEGG not available
>>
>>> summary(as(keggResults, "HyperGResult"))
>>>
>>     KEGGID      Pvalue OddsRatio   ExpCount Count Size
>> 1   04977 0.003627659 26.245614 0.09151194     2   23
>> 2   04744 0.005355471 21.178138 0.11140584     2   28
>> 3   05216 0.005738421 20.389864 0.11538462     2   29
>> 4   04620 0.006476798  9.056140 0.38992042     3   98
>> 5   05020 0.007834917 17.187500 0.13527851     2   34
>> 6   00830 0.015235568 11.924485 0.19098143     2   48
>> 7   04621 0.021800737  9.776316 0.23076923     2   58
>> 8   00982 0.022512006  9.602955 0.23474801     2   59
>> 9   05214 0.026211199  8.820034 0.25464191     2   64
>> 10  00232 0.027536679 43.758333 0.02785146     1    7
>> 11  04720 0.030141245  8.153967 0.27453581     2   69
>> 12  04666 0.048955554  6.183014 0.35809019     2   90
>>
>>
>> Specifically, the error is thrown in the call to getAnnMap
>>
>> I don't currently have a local installation of bioc-devel 3.0 yet (mea
>> culpa) but a quick glance at the source code tells me that the relevant
>> summary method still calls getAnnMap with "KEGG" as it's second argument.
>>
>>
>> Thanks,
>> ~G
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis

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