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[Bioc-devel] KEGG.db

3 messages · Setia Pramana, Willem Ligtenberg, Marc Carlson

Setia Pramana
# 
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
Willem Ligtenberg
# 
Hi,

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,

Willem
On Mon, May 7, 2012 at 9:30 AM, Setia Pramana <setia.pramana at ki.se> wrote:
1 day later
Marc Carlson
# 
Willem is right.  The as.list() method you want is the one from 
AnnotationDbi.  Other as.list methods will not know what to do with the 
bimap object in question.  So in the usage context you are dexcribing, 
you may need to import that method in your NAMESPACE file so that your 
package knows about it.

Also, the KEGG.db package has not been able to be updated for over a 
year now.  The reactome.db package is probably a good alternative.


   Marc
On 05/07/2012 12:38 AM, Willem Ligtenberg wrote: