[BioC] Kegg Profile package problem

[Dan Tenenbaum]

On Thu, Dec 27, 2012 at 4:30 AM, gregory voisin <voisingreg at yahoo.fr> wrote:
> Hi Dan ,
> Yes, the link associated to hsa00910 doesn't exist but the map00910
> (http://www.genome.jp/kegg/pathway/map/map00910.html) exists
>
> The id 00910 is a result provided by the find_enriched_pathway function().
>

In that case, can you get the pathway map you need from this link:

http://www.genome.jp/kegg/pathway/map/map00910.png


?

Dan

> Greg
>
>
>
> ________________________________
> De : Dan Tenenbaum <dtenenba at fhcrc.org>
> À : gregory voisin <voisingreg at yahoo.fr>
> Cc : "bioconductor at r-project.org" <bioconductor at r-project.org>
> Envoyé le : Jeudi 27 décembre 2012 2h35
> Objet : Re: [BioC] Kegg Profile package problem
>
> On Wed, Dec 26, 2012 at 6:54 AM, gregory voisin <voisingreg at yahoo.fr> wrote:
>>
>>
>>
>> Hi,
>> I use KeggProfile in my pipeline analysis and it's efficient, but I have
>> problem with one pathway_ID.
>>
>> Exemple ( copy and paste):
>>
>> require(KEGGprofile)
>> download_KEGGfile(pathway_id="04110",specis='hsa')
>>
>> #In this case , not problem
>>
>> download_KEGGfile(pathway_id="00910",specis='hsa')
>
>
> I think perhaps there is no such pathway. Here's a list of all human
> pathways:
> http://rest.kegg.jp/list/pathway/hsa
>
> 04110 is included but 00910 is not.
>
> Dan
>
>
>>
>> #this pahway exits in KEGG, but the download is impossible
>> #[1] "Downloading files: 1/1"
>> #essai de l'URL
>> 'http://www.genome.jp/kegg-bin/download?entry=hsa00910&format=kgml'
>> #Content type 'text/plain' length unknown
>> #URL ouverte
>> #downloaded 1 bytes
>>
>> #essai de l'URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png'
>> #Erreur dans download.file(paste("http://www.genome.jp/kegg/pathway/",
>> specis,  :
>> #  impossible d'ouvrir l'URL
>> 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png'
>> #De plus : Message d'avis :
>> #In download.file(paste("http://www.genome.jp/kegg/pathway/", specis,  :
>> #  ouverture impossible : le statut HTTP était '404 Not Found'
>>
>>
>> My solution :  omit this pathway in my analysis: ponctual, fast  but not
>> very elegant and not professional !!
>>
>> If someone has a suggestion , comments or solution, let's go ,
>>
>> Thanks
>>
>> Greg
>> Montréal
>>
>>        [[alternative HTML version deleted]]
>>
>>
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>
>