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Question: Using pathview with uncommon species leads to Errors
0
gravatar for rafre
16 months ago by
rafre0
rafre0 wrote:

Hello together,

I want to plot my RNA-Seq data to the Corynebacterium glutamicum ATCC13032 (Bielefeld) KEGG pathway, but unfortunatly this is not working wiht my organism. I found an example for B. subtilis which is working pretty fine, but changing the species name ( i looked it up in the data(korg)) leads to an error.

library(pathview)
> bsu.dat.kegg <- sim.mol.data(mol.type="gene"
+                              ,id.type="kegg"
+                              ,species="bsu"
+                              ,nmol=3000)
> 
>     pv.out.bs <- pathview(gene.data = bsu.dat.kegg
+                        , gene.idtype="kegg"
+                        , pathway.id = "00010"
+                        , species = "bsu"
+                        , out.suffix = "bsu.kegg")
Info: Working in directory C:/Users/....
Info: Writing image file bsu00010.bsu.kegg.png
> cgb.dat.kegg <- sim.mol.data(mol.type="gene"
+                              ,id.type="kegg"
+                              ,species="cgb"
+                              ,nmol=3000)
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  Bad Request (HTTP 400).
> traceback()
5: stop(http_condition(x, "error", task = task, call = call))
4: stop_for_status(response)
3: .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
2: keggConv("ncbi-geneid", species)
1: sim.mol.data(mol.type = "gene", id.type = "kegg", species = "cgb", 
       nmol = 3000)
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] pathview_1.12.0      org.Hs.eg.db_3.3.0   AnnotationDbi_1.34.4 IRanges_2.6.1        S4Vectors_0.10.2    
[6] Biobase_2.32.0       BiocGenerics_0.18.0 

loaded via a namespace (and not attached):
 [1] KEGGgraph_1.30.0  XML_3.98-1.4      Biostrings_2.40.2 png_0.1-7         R6_2.1.2          grid_3.3.1       
 [7] DBI_0.4-1         RSQLite_1.0.0     httr_1.2.1        graph_1.50.0      zlibbioc_1.18.0   curl_0.9.7       
[13] XVector_0.12.0    Rgraphviz_2.16.0  tools_3.3.1       KEGGREST_1.12.2  

Somehow the download of KEGGpathways is possible with the species ID.

download.keggpathway.id = "01100"
              , species = "cgb"
              , kegg.dir = myDir
              , file.type=c("xml", "png"))

I hope you can reproduce my Error or show me a way out

Thanks in advance

ADD COMMENTlink modified 16 months ago by Luo Weijun1.4k • written 16 months ago by rafre0
1
gravatar for Luo Weijun
16 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
It appears to be a KEGG REST API problem. I noticed that KEGG REST API had some issue lately as shown in the build error of the package: http://bioconductor.org/checkResults/release/bioc-LATEST/KEGGREST/ You can check this again when the build error is gone.
ADD COMMENTlink written 16 months ago by Luo Weijun1.4k
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