Problem to download Kegg map from KEGGprofile package
0
0
Entering edit mode
@gregory-voisin-945
Last seen 6.3 years ago
Canada
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') #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 > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=French_Canada.1252  LC_CTYPE=French_Canada.1252 [3] LC_MONETARY=French_Canada.1252 LC_NUMERIC=C [5] LC_TIME=French_Canada.1252 attached base packages: [1] stats     graphics  grDevices utils     datasets  methods   base other attached packages:  [1] KEGGprofile_1.0.0    KEGG.db_2.8.0        RSQLite_0.11.2  [4] DBI_0.2-5            AnnotationDbi_1.20.0 Biobase_2.18.0  [7] BiocGenerics_0.4.0   TeachingDemos_2.8    png_0.1-4 [10] XML_3.95-0.1 loaded via a namespace (and not attached): [1] IRanges_1.16.2  parallel_2.15.0 stats4_2.15.0 [[alternative HTML version deleted]]
GO KEGGprofile GO KEGGprofile • 796 views
ADD COMMENT

Login before adding your answer.

Traffic: 486 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6