[BioC] KEGGSOAP incomplete list.pathways
mcarlson at fhcrc.org
Sat Nov 19 01:32:30 CET 2011
Thank you for reporting this. But I fear you are probbaly reporting
this to the wrong group. The KEGGSOAP package is unlike most other
bioconductor annotation packages in that it is actually a thin wrapper
around KEGGs SOAP API. The discrepancy you are seeing is generated by
their two SOAP methods. I actually have no idea why list.pathways
(which is really the list_pathways method from their API), does not
return "path:ath00630", but I bet that they would like to know this is
This is the site that describes their API:
And this is probably who you should contact:
Now that warning that you saw was coming from the XML package, (which
KEGGSOAP depends on to learn about the existence of all these methods).
The warning means that XML might be causing us some other trouble too
(which we are investigating), but it is probably not going to cause the
kind of trouble you described here.
On 11/18/2011 01:34 PM, kevin [guest] wrote:
> I'm finding a discrepancy with KEGGSOAP for arabidopsis. Not all the pathways are returned via list.pathways. I'm trying to get the text definition of identified pathways
> for example:
>  "path:ath00630" "path:ath01100"
> yet 00630 is not within the 63 pathways:
>  "path:ath00603"
>  "path:ath00620"
>  "path:ath00640"
>  "path:ath00660"
>  "path:ath00710"
> I do get a warning:
> Warning message:
> In matrix(unlist(.SOAP(KEGGserver, "list_pathways", .soapArgs = list(org = org), :
> data length  is not a sub-multiple or multiple of the number of rows 
> thanks for the help, and let me know if you need more information,
> -- output of sessionInfo():
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-pc-linux-gnu (64-bit)
>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>  LC_PAPER=C LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  SSOAP_0.8-0 org.At.tair.db_2.6.4 RSQLite_0.10.0
>  DBI_0.2-5 AnnotationDbi_1.16.2 Biobase_2.14.0
>  KEGGSOAP_1.28.0
> loaded via a namespace (and not attached):
>  IRanges_1.12.1 RCurl_1.7-0 XML_3.4-3 XMLSchema_0.1-6
> Sent via the guest posting facility at bioconductor.org.
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> Bioconductor at r-project.org
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