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
--
Computational Biologist
Genentech Research
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