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

[Saroj K Mohapatra]

Perhaps v2 returns the common pathway between both genes?

Saroj


Julien Meunier wrote:
>
> 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.
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: 
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>