enrichMKEGG can not identify the species
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bright602 • 0
@bright602-14940
Last seen 3.2 years ago

Hi there,

Recently I tried to use enrichMKEGG or enrichKEGG function from clusterProfiler, however, there is an error message stating that

Error in download.KEGG.Module(species) :
  'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'...

Even I tried to to use the example from vignette, and still have the same problem.

library(clusterProfiler)
data("geneList")                    
xx <- enrichMKEGG(de, organism = 'hsa', head(summary(xx)))

Could anyone give me some suggestions?

 

Thanks,

Sim

 

 

clusterprofiler • 1.2k views
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Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 4 days ago
Wageningen University, Wageningen, the …

You did not define the object de, which you used as input. Also, the last line of your code is weird; why do you include head(summary(xx))?

 

Example from vignette is running fine for me (please note my comments):

> library(clusterProfiler)
> data(geneList, package='DOSE')
> de <- names(geneList)[1:100]
>
> # run function enrichKEGG (for KEGG categories)
>
> yy <- enrichKEGG(de, organism='hsa', pvalueCutoff=0.01)
> head(yy)
               ID                             Description GeneRatio  BgRatio       pvalue
hsa04110 hsa04110                              Cell cycle      8/46 124/7431 7.353075e-07
hsa04218 hsa04218                     Cellular senescence      7/46 160/7431 4.970308e-05
hsa04114 hsa04114                          Oocyte meiosis      6/46 124/7431 1.037461e-04
hsa04657 hsa04657                 IL-17 signaling pathway      5/46  93/7431 2.518699e-04
hsa04914 hsa04914 Progesterone-mediated oocyte maturation      5/46  99/7431 3.371863e-04
             p.adjust       qvalue                               geneID Count
hsa04110 8.088382e-05 7.662678e-05 8318/991/9133/890/983/4085/7272/1111     8
hsa04218 2.733669e-03 2.589792e-03    2305/4605/9133/890/983/51806/1111     7
hsa04114 3.804024e-03 3.603812e-03         991/9133/983/4085/51806/6790     6
hsa04657 6.926423e-03 6.561874e-03             4312/6280/6279/6278/3627     5
hsa04914 7.418099e-03 7.027673e-03               9133/890/983/4085/6790     5
>
>
> # run function enrichMKEGG (for KEGG modules)
> # note p-value cutoff has been increased to
> # p=0.1, because otherwise no modules pass cutoff.
>
> zz <- enrichMKEGG(de, organism='hsa',  pvalueCutoff=0.1)
> head(zz)
           ID   Description GeneRatio BgRatio     pvalue   p.adjust qvalue geneID Count
M00389 M00389 APC/C complex       1/7 14/1522 0.06275953 0.06275953     NA    991     1
>

 

> sessionInfo()
R version 3.5.1 Patched (2018-07-12 r74967)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] 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] clusterProfiler_3.8.1 BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] ggrepel_0.8.0        Rcpp_0.12.17         lattice_0.20-35      tidyr_0.8.1         
 [5] GO.db_3.6.0          assertthat_0.2.0     digest_0.6.15        ggforce_0.1.3       
 [9] R6_2.2.2             plyr_1.8.4           ggridges_0.5.0       stats4_3.5.1        
[13] RSQLite_2.1.1        ggplot2_3.0.0        pillar_1.3.0         rlang_0.2.1         
[17] lazyeval_0.2.1       data.table_1.11.4    blob_1.1.1           S4Vectors_0.18.3    
[21] Matrix_1.2-14        qvalue_2.12.0        splines_3.5.1        BiocParallel_1.14.2
[25] stringr_1.3.1        igraph_1.2.1         bit_1.1-14           munsell_0.5.0       
[29] fgsea_1.6.0          compiler_3.5.1       pkgconfig_2.0.1      BiocGenerics_0.26.0
[33] tidyselect_0.2.4     tibble_1.4.2         gridExtra_2.3        IRanges_2.14.10     
[37] enrichplot_1.0.2     viridisLite_0.3.0    crayon_1.3.4         dplyr_0.7.6         
[41] MASS_7.3-50          grid_3.5.1           gtable_0.2.0         DBI_1.0.0           
[45] magrittr_1.5         units_0.6-0          scales_0.5.0         stringi_1.2.3       
[49] GOSemSim_2.6.0       reshape2_1.4.3       viridis_0.5.1        bindrcpp_0.2.2      
[53] DO.db_2.9            rvcheck_0.1.0        cowplot_0.9.3        fastmatch_1.1-0     
[57] tools_3.5.1          bit64_0.9-7          Biobase_2.40.0       glue_1.3.0          
[61] tweenr_0.1.5         purrr_0.2.5          ggraph_1.0.2         parallel_3.5.1      
[65] AnnotationDbi_1.42.1 colorspace_1.3-2     UpSetR_1.3.3         DOSE_3.6.1          
[69] memoise_1.1.0        bindr_0.1.1         
>
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Thanks Guido, I tried to repeat but the same error message still pop out.

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> library(clusterProfiler)
> data(geneList, package='DOSE')
> de <- names(geneList)[1:100]
> yy <- enrichKEGG(de, organism='hsa', pvalueCutoff=0.01)
Error in download.KEGG.Path(species) :
  'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'...

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> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] org.Hs.eg.db_3.6.0      GSEABase_1.43.0         annotate_1.59.0        
 [4] XML_3.98-1.12           GO.db_3.6.0             DOSE_3.7.1             
 [7] BiocManager_1.30.1      RDAVIDWebService_1.19.0 GOstats_2.47.0         
[10] Category_2.47.0         Matrix_1.2-14           AnnotationDbi_1.43.1   
[13] IRanges_2.15.14         S4Vectors_0.19.17       Biobase_2.41.1         
[16] graph_1.59.0            BiocGenerics_0.27.1     clusterProfiler_3.9.1  
[19] ggplot2_3.0.0           ChIPseeker_1.17.0      

 
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Mmm, looks like you have a mix of release and development packages.... For R-3.5.x / Bioc-3.7 you should use clusterProfiler version 3.8.1 (here) (2nd number = an even number) , you have version 3.9.1 (2nd number = an odd number, thus the 'development' version). Maybe this explains your error; again, your code is running fine for me.... Please note that you have multiple dev packages installed

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Thanks for reply. I will look into that and have a try.
 

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