[Bioc-devel] KEGG.db

Willem Ligtenberg willem.ligtenberg at openanalytics.eu
Mon May 7 09:38:19 CEST 2012


Although I am not sure if you should be using the KEGG.db package any
more, since it is deprecated.
See the following message when you load the KEGG.db package:
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.  One possible alternative to consider is to look at the
  reactome.db package

You should make sure, your package uses the right as.list method. You
can do this by using:
AnnotationDbi::as.list instead of just as.list. (This specifies the
package from which it should load the function.)

Kind regards,


On Mon, May 7, 2012 at 9:30 AM, Setia Pramana <setia.pramana at ki.se> wrote:
> Hi All,
> I am developing a new package using the info from KEGG.db. I used the following command to map  KEGG pathway identifiers to Entrez Gene:
>  mapped.genes <-as.list(KEGGPATHID2EXTID)
> When I run the function  as an R package, I have the following error msg:
> Error in as.list.default(KEGGPATHID2EXTID) :
>  no method for coercing this S4 class to a vector
> However when I run not as a package (like normal R function), the function works well.
> Please help me to find out what may be the problem.
> Thank you in advance for your help.
> Best,
> Setia
> MEB KI Stockholm
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