[BioC] Retrieving KEGG pathway diagrams via KEGGSOAP

Saroj K Mohapatra smohapat at vbi.vt.edu
Fri Apr 17 04:02:50 CEST 2009

Hi Daren,

I do not know why but if you try with more than one node, the code works.

> url <- mark.pathway.by.objects("path:hsa03050", 
 c("hsa:5709", "hsa:10197"))
> url
[1] "http://soap.genome.jp/tmp/mark_pathway_www2_api15820/hsa03050.gif"

> if(interactive()){ browseURL(url) }



----- Original Message -----
From: "Daren Tan" <darentan76 at gmail.com>
To: bioconductor at stat.math.ethz.ch
Sent: Thursday, April 16, 2009 8:46:30 PM GMT -05:00 US/Canada Eastern
Subject: [BioC] Retrieving KEGG pathway diagrams via KEGGSOAP

There was an earlier example about KEGGSOAP, which I am looking for
all this while. My work centers around hsa, so I tried one of the
pathway annotated in human and sound genes. However, NULL is always
returned. What is wrong ?

> get.genes.by.pathway("path:hsa03050")
 [1] "hsa:100132108" "hsa:10197"     "hsa:10213"     "hsa:121906"
"hsa:122706"    "hsa:143471"    "hsa:23198"     "hsa:345645"
[10] "hsa:51371"     "hsa:5682"      "hsa:5683"      "hsa:5684"
"hsa:5685"      "hsa:5686"      "hsa:5687"      "hsa:5688"
[19] "hsa:5690"      "hsa:5691"      "hsa:5692"      "hsa:5693"
"hsa:5694"      "hsa:5695"      "hsa:5696"      "hsa:5698"
[28] "hsa:5700"      "hsa:5701"      "hsa:5702"      "hsa:5704"
"hsa:5705"      "hsa:5706"      "hsa:5707"      "hsa:5708"
[37] "hsa:5710"      "hsa:5713"      "hsa:5714"      "hsa:5717"
"hsa:5718"      "hsa:5719"      "hsa:5720"      "hsa:5721"
[46] "hsa:7979"      "hsa:9491"      "hsa:9861"
> url <- mark.pathway.by.objects("path:hsa03050", "hsa:10197")
> url
> url <- mark.pathway.by.objects("path:hsa03050", "hsa:5684")
> url

> sessionInfo()
R version 2.8.1 (2008-12-22)

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
[1] KEGGSOAP_1.16.0 SSOAP_0.4-6     RCurl_0.94-1    XML_2.1-0
limma_2.16.4    RSQLite_0.7-1   DBI_0.2-4

loaded via a namespace (and not attached):
[1] gdata_2.4.2    gplots_2.6.0   gtools_2.5.0-1 tools_2.8.1

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