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Question: Please help with pathway analysis using Pathview
0
gravatar for Sara
17 months ago by
Sara0
Sara0 wrote:

Hi all,

I'm just learning to work with Pathview package, it sounds great, however, I had a problem with it. Hope it is solved here. I used the following command:

pv.out <- pathview(gene.data = df[,1], pathway.id = "00906", species = "ath", out.suffix = "df", kegg.native = T)

I used Entrez ID for gene ID type, the head of my "df" file is like below:

   ​ ID     logFC
1   824011 10.790438
2   820667  9.013788
3   838887  9.793571
4   838504  9.715823
5 10723101  8.816703
6   830443  8.663770

Among the above gene ID, one of them is involved in the Carotenoid biosynthesis pathway (pathway Id of "00906"), but the software told "Note: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong". Here is the output of the above command:

 

Info: Getting gene ID data from KEGG...
Info: Done with data retrieval!
Info: Downloading xml files for ath00906, 1/1 pathways..
Info: Downloading png files for ath00906, 1/1 pathways..
Note: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Info: Working in directory C:/Users/dps/Documents
Info: Writing image file ath00906.df.png

Also, the sessionInfo() is below:

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=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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] pathview_1.10.1      org.Hs.eg.db_3.2.3   RSQLite_1.0.0        DBI_0.4-1            AnnotationDbi_1.32.3 IRanges_2.4.8        S4Vectors_0.8.11    
[8] Biobase_2.30.0       BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
 [1] KEGGgraph_1.28.0  XML_3.98-1.4      Biostrings_2.38.4 png_0.1-7         R6_2.1.2          grid_3.3.1        httr_1.2.0        graph_1.48.0      zlibbioc_1.16.0  
[10] curl_0.9.7        XVector_0.10.0    Rgraphviz_2.14.0  tools_3.3.1       KEGGREST_1.10.1  

 

Could you please help me out to solve the problem?

Thank you

 
ADD COMMENTlink modified 17 months ago by Luo Weijun1.4k • written 17 months ago by Sara0
0
gravatar for Luo Weijun
17 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
You need to convert ID from numeric to character first., something like: gids= as.character(df[,1]) pv.out <- pathview(gene.data =gids, pathway.id = "00906", species = "ath", out.suffix = "df", kegg.native = T)
ADD COMMENTlink written 17 months ago by Luo Weijun1.4k

Thank you, Luo. It works fine. 

ADD REPLYlink written 17 months ago by Sara0
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