[Bioc-devel] error in summary method for KEGGHyperGResult

[James W. MacDonald]

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