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
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