Question: compareCluster on Mus musculus
0
gravatar for unamourdeswann
10 months ago by
unamourdeswann10 wrote:

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 • 344 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by unamourdeswann10
Answer: compareCluster on Mus musculus
1
gravatar for unamourdeswann
10 months ago by
unamourdeswann10 wrote:

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!

ADD COMMENTlink modified 10 months ago • written 10 months ago by unamourdeswann10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 189 users visited in the last hour