[BioC] KEGGSOAP: problem with get.pathways.by.genes()

[Julien Meunier]

Hi Saroj,


Thank you for your reply. Yet, I am still puzzled by the behavior of
get.pathway.by.genes() in KEGGSOAP:


I have been running this session:

 > sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] KEGG.db_2.2.11      RSQLite_0.7-1       DBI_0.2-4
[4] AnnotationDbi_1.6.0 Biobase_2.4.1       RCurl_0.94-1
[7] KEGGSOAP_1.18.0

loaded via a namespace (and not attached):
[1] SSOAP_0.4-6 XML_2.3-0



and the following code:

My.entrez2pathid<-function(refseqid){

   require(KEGG.db)
   stopifnot(is.character(refseqid))
   v<-mget(refseqid,KEGGEXTID2PATHID,ifnotfound=NA)

   return(v)

}

v1<-My.entrez2pathid(c("16185","11652"))


would give this result


 > v1
$`16185`
[1] "mmu04060" "mmu04630"

$`11652`
  [1] "mmu04010" "mmu04012" "mmu04150" "mmu04210" "mmu04370" "mmu04510"
  [7] "mmu04530" "mmu04620" "mmu04630" "mmu04660" "mmu04662" "mmu04664"
[13] "mmu04910" "mmu04920" "mmu05210" "mmu05211" "mmu05212" "mmu05213"
[19] "mmu05214" "mmu05215" "mmu05218" "mmu05220" "mmu05221" "mmu05222"
[25] "mmu05223"


whereas

My.ksoap.entrez2pathid<-function(refseqid){

   require(KEGGSOAP)
   stopifnot(is.character(refseqid))
   v<-get.pathways.by.genes(refseqid)

   return(v)

}

v2<-My.ksoap.entrez2pathid(c("mmu:16185","mmu:11652"))


returns

 > v2
[1] "path:mmu04630"



Checking on the KEGG website, the refseq id 11652 is associated with
a lot of pathways (those returned in "v1").


Does anybody knows why KEGGSOAp seems to fail to retrieve all the pathways ?


Many thanks,
Julien





Saroj K Mohapatra wrote:
> Hi Julien:
> 
> For some reason, if you use more than one gene, the function does return 
> the pathways.
> 
>  > get.pathways.by.genes(c("mmu:11479"))
> character(0)
>  >
>  > get.pathways.by.genes(c("mmu:11479", "mmu:11477"))
> [1] "path:mmu04060" "path:mmu04350"
> 
> Best,
> 
> Saroj
> 
> 
> Julien Meunier wrote:
>>
>>
>> Hi everyone,
>>
>> I am trying to convert entrez id (mouse) to KEGG pathway
>> using the keggsoap package, and having a hard time.
>>
>>
>> get.genes.by.pathway(c("path:mmu04060"))
>>
>> would give me the following result:
>>
>> [1] "mmu:100044793" "mmu:100047704" "mmu:110542"    "mmu:11477" 
>> "mmu:11479" ...
>>
>>
>>
>> However, the following
>>
>> get.pathways.by.genes(c("mmu:11479"))
>>
>> returns character(0)
>>
>>
>> I also tested get.pathways.by.genes with the IL2 gene (entrez id 16183)
>> involved in several pathways, calling the function with "16183",
>> "mmu:16183" and other variations with the same result.
>>
>> The vignette mentioned they might be "problem on the server side" with
>> get.pathways.by.genes(), and I googled without succes.
>>
>>
>> Any ideas to get this function to work ?
>>
>>
>> Thank you for your time,
>> Julien
>>
>>
>> PS: I known I can use KEGG.db or org.Mm.eg.db, or other locale packages
>> but for some reason I would rather use an online query.
>>
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>>
>