[Bioc-devel] SemSim package - Finding semantic similarity between GO terms

Herve Pages hpages at fhcrc.org
Mon Jan 8 21:47:09 CET 2007

Hi Tim,

Tim Smith wrote:
> Hi,
> I was trying to work with the SemSim package for windows. I downloaded the package for windows from the bioconductor website, but when I try to reproduce the examples given in the vignette, I get errors. For example:
>>   geneSim("852695", "5261")
> Error in .getOnt(gene1, wh_ont, drop) : object ".id2go" not found
> Do I need some other packages before the SemSim package will work?

If you were able to load the package, then you should be all set.
The .id2go object is created in the package environment at load-time.
You should be able to see it with:

  > library(SemSim)
  > ls("package:SemSim", all.names=TRUE)
   [1] ".First.lib"   "geneSim"      ".getOnt"      ".gocount"     "GOCount"
   [6] ".id2go"       "mgeneSim"     "mtermSim"     ".packageName" "termSim"

Which version of SemSim are you using?
Could you please provide the output of sessionInfo() along with the complete
set of commands that you did between
  geneSim("852695", "5261")


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