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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