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kjboteroo
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@kjboteroo-10699
Last seen 7.9 years ago
Dears all,
I need get the reactions for a organism. I am using KEGGREST for that. In the manual of KEGGREST says that I can use keggList(database, organism), but I am trying the following way and I can't:
> keggList("reaction", "hsa")
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) :
Bad Request (HTTP 400).
> traceback()
4: stop(http_condition(x, "error", task = task, call = call))
3: stop_for_status(response)
2: .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
1: keggList("reaction", "hsa")
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=es_CO.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=es_CO.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_CO.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=es_CO.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] KEGGREST_1.12.1
loaded via a namespace (and not attached):
[1] zlibbioc_1.18.0 httr_1.1.0 R6_2.1.2 IRanges_2.6.0 XVector_0.12.0
[6] parallel_3.3.0 tools_3.3.0 curl_0.9.7 Biostrings_2.40.0 S4Vectors_0.10.0
[11] BiocGenerics_0.18.0 stats4_3.3.0 png_0.1-7
I reviewed others forums, I installed R 3.3 and I have actualized KEGGREST and BiocInstaller, but nothing works. I wonder if is not possible to obtain the reaction for specific organism with KEGGREST, or exist other solution?
Thanks
The documentation for the REST API (see the section "Entry list") is a little unclear. Seems to suggest that maybe /list/reaction/hsa (what your code translates to) is possible, but it isn't.
You can just say:
keggList("reaction")to get a list of all reactions (equivalent to /list/reaction).
If this behavior is not what you expect, you can contact KEGG and see what they say.