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Question: Possible bug: outdated result from listDatabases()
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gravatar for olj23
3 months ago by
olj230
olj230 wrote:

Possibly outdated result from listDatabases()

According to the KEGG API docs (which are linked in the function's documentation), the following databases are available:

pathway | brite | module | ko | genome | <org> | vg | ag | compound |
glycan | reaction | rclass | enzyme | disease | drug | dgroup | environ |
genes | ligand | kegg | <medicus> | <outside>

Indeed, calls can be made to any of these databases using keggFind, keggGet etc.

However, listDatabases() returns the following list instead:

 [1] "pathway"  "brite"    "module"   "disease"  "drug"     "environ"  "ko"       "genome"   "compound"
[10] "glycan"   "reaction" "rclass"   "enzyme"   "organism"

Note that:

  • vg, ag, dgroup, genes, ligand are available but not listed
  • organism is listed but not available

The function output may require updating.

ADD COMMENTlink modified 3 months ago by daniel.vantwisk30 • written 3 months ago by olj230
2
gravatar for daniel.vantwisk
3 months ago by
daniel.vantwisk30 wrote:

Thanks for the notice!  I've made the fix.  The output to listDatabases() now returns the appropriate results in the current release version of KEGGREST(v1.16.1).

ADD COMMENTlink modified 3 months ago • written 3 months ago by daniel.vantwisk30
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