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

[Saroj K Mohapatra]

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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