compareCluster on Mus musculus
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Entering edit mode
@unamourdeswann-12423
Last seen 2.8 years ago
France

Hello everyone.

I probably mistyped something, but I cannot use compareCluster on my data (Mouse mm10).

Here is a minimal example (using R --vanilla):

library(clusterProfiler)
[...]
l <- c("14654", "224897", "56463",  "53623", "57875", "22245", "54610", "224997", "15162",  "26438", "76889", "14389", "80707", "268379", "268859", "215999", "22295", "17289")
compareCluster(geneCluster=l, fun="enrichKEGG", organism="mmu", pvalueCutoff=0.05, pAdjustMethod="BH")

And I get:

The following `from` values were not present in `x`: .id
Error in `$<-.data.frame`(`*tmp*`, "Cluster", value = integer(0)) :
  replacement has 0 rows, data has 31

Using:

compareCluster(geneCluster=l, fun="enrichKEGG", organism="hsa", pvalueCutoff=0.05, pAdjustMethod="BH")

works fine (although no enrichment is found).

Using library(org.Mm.eg.db) beforehand does not seem to help.

Package clusterProfiler seems up to date (3.10.0). Session info gives:

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.10

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] clusterProfiler_3.10.0

loaded via a namespace (and not attached):
 [1] Biobase_2.42.0       viridis_0.5.1        httr_1.4.0          
 [4] tidyr_0.8.2          bit64_0.9-7          jsonlite_1.6        
 [7] viridisLite_0.3.0    splines_3.5.1        ggraph_1.0.2        
[10] assertthat_0.2.0     DO.db_2.9            rvcheck_0.1.3       
[13] triebeard_0.3.0      urltools_1.7.1       stats4_3.5.1        
[16] blob_1.1.1           progress_1.2.0       ggrepel_0.8.0       
[19] pillar_1.3.1         RSQLite_2.1.1        lattice_0.20-38     
[22] glue_1.3.0           digest_0.6.18        RColorBrewer_1.1-2  
[25] qvalue_2.14.0        colorspace_1.3-2     cowplot_0.9.3       
[28] Matrix_1.2-15        plyr_1.8.4           pkgconfig_2.0.2     
[31] purrr_0.2.5          GO.db_3.7.0          scales_1.0.0        
[34] ggplotify_0.0.3      europepmc_0.3        tweenr_1.0.1        
[37] enrichplot_1.2.0     BiocParallel_1.16.2  ggforce_0.1.3       
[40] tibble_1.4.2         farver_1.1.0         IRanges_2.16.0      
[43] ggplot2_3.1.0        UpSetR_1.3.3         BiocGenerics_0.28.0
[46] lazyeval_0.2.1       magrittr_1.5         crayon_1.3.4        
[49] memoise_1.1.0        DOSE_3.8.0           MASS_7.3-51.1       
[52] xml2_1.2.0           prettyunits_1.0.2    tools_3.5.1         
[55] data.table_1.11.8    hms_0.4.2            stringr_1.3.1       
[58] S4Vectors_0.20.1     munsell_0.5.0        AnnotationDbi_1.44.0
[61] bindrcpp_0.2.2       compiler_3.5.1       gridGraphics_0.3-0  
[64] rlang_0.3.0.1        ggridges_0.5.1       units_0.6-2         
[67] grid_3.5.1           igraph_1.2.2         gtable_0.2.0        
[70] DBI_1.0.0            reshape2_1.4.3       R6_2.3.0            
[73] gridExtra_2.3        dplyr_0.7.8          bit_1.1-14          
[76] bindr_0.1.1          fastmatch_1.1-0      fgsea_1.8.0         
[79] GOSemSim_2.8.0       stringi_1.2.4        parallel_3.5.1      
[82] Rcpp_1.0.0           tidyselect_0.2.5    

What did I miss?  Thank you all!

clusterprofiler • 3.6k views
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1
Entering edit mode
@unamourdeswann-12423
Last seen 2.8 years ago
France

D'oh!

Using:

compareCluster(geneCluster=list("1"=l), fun="enrichKEGG", organism="mmu", pvalueCutoff=0.05, pAdjustMethod="BH")`

works perfectly fine (geneCluster obviously expects a list of genes).

Sorry to everyone!

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