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Question: Accessing KEGG (errors w/ KEGGREST)
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gravatar for sampsonj74
10 months ago by
sampsonj740
sampsonj740 wrote:

Dear All-

I am trying to access the KEGG database from R.  I downloaded KEGGREST (as I've never done this before, I'm more than willing to use any package, but this seemed best). However, I copied/pasted a couple sample commands from their reference file and received errors. Did I make a mistake...is there a better way to access KEGG from R.

Josh

 

################################################################################################

library("KEGGREST")

keggList("pathway","hsa")
keggFind("genes", c("shiga", "toxin")) 

################################################################################################

 

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] KEGGREST_1.8.1       BiocInstaller_1.18.5 randomForest_4.6-12 

loaded via a namespace (and not attached):
 [1] zlibbioc_1.14.0     httr_1.2.1          R6_2.2.0            IRanges_2.2.9       XVector_0.8.0       parallel_3.2.1      tools_3.2.1         curl_2.3           
 [9] Biostrings_2.36.4   S4Vectors_0.6.6     BiocGenerics_0.14.0 stats4_3.2.1        png_0.1-7          
> library("KEGGREST")

> keggList("pathway","hsa")
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  invalid request, server returned Success: (200) OK (http://rest.kegg.jp/list/pathway/hsa)
> keggFind("genes", c("shiga", "toxin"))
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  invalid request, server returned Success: (200) OK (http://rest.kegg.jp/find/genes/shiga+toxin)

ADD COMMENTlink modified 10 months ago by Gordon Smyth32k • written 10 months ago by sampsonj740
0
gravatar for Gordon Smyth
10 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

You can access KEGG using basic R commands. For example:

> Pathways <- read.table("http://rest.kegg.jp/list/pathway/hsa", quote="", sep="\t")
> head(Pathways)
             V1                                                              V2
1 path:hsa00010             Glycolysis / Gluconeogenesis - Homo sapiens (human)
2 path:hsa00020                Citrate cycle (TCA cycle) - Homo sapiens (human)
3 path:hsa00030                Pentose phosphate pathway - Homo sapiens (human)
4 path:hsa00040 Pentose and glucuronate interconversions - Homo sapiens (human)
5 path:hsa00051          Fructose and mannose metabolism - Homo sapiens (human)
6 path:hsa00052                     Galactose metabolism - Homo sapiens (human)

will read all the human KEGG pathway IDs and names into a data.frame.

 

ADD COMMENTlink modified 10 months ago • written 10 months ago by Gordon Smyth32k

Gordon-

Thank you very much! This is quite helpful.

Josh

ADD REPLYlink written 10 months ago by sampsonj740
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