[BioC] KEGGSOAP incomplete list.pathways

[Marc Carlson]

Hi Kevin,

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 
happening.

This is the site that describes their API:
http://www.genome.jp/kegg/docs/keggapi_manual.html#label:36

And this is probably who you should contact:
http://www.genome.jp/kegg/anniversary/contact.html


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.


   Marc




On 11/18/2011 01:34 PM, kevin [guest] wrote:
> hi,
>
>    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:
> get.pathways.by.genes('ath:AT5G14780')
> [1] "path:ath00630" "path:ath01100"
>
> yet 00630 is not within the 63 pathways:
> [1] "path:ath00603"
> [1] "path:ath00620"
>
> [1] "path:ath00640"
> [1] "path:ath00660"
> [1] "path:ath00710"
>
>   I do get a warning:
> Warning message:
> In matrix(unlist(.SOAP(KEGGserver, "list_pathways", .soapArgs = list(org = org),  :
>    data length [125] is not a sub-multiple or multiple of the number of rows [63]
>
> thanks for the help, and let me know if you need more information,
> kevin
>
>
>   -- output of sessionInfo():
>
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] SSOAP_0.8-0          org.At.tair.db_2.6.4 RSQLite_0.10.0
> [4] DBI_0.2-5            AnnotationDbi_1.16.2 Biobase_2.14.0
> [7] KEGGSOAP_1.28.0
>
> loaded via a namespace (and not attached):
> [1] 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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