clusterProfiler Results not showing

Question

[geoffkerr22]

Hello,

I am having some issues with clusterProfiler and the enrichKEGG function. Here is my code:

library(clusterProfiler)

kegg_enrich <- enrichKEGG(gene = results_sig_entrez$entrez,
                          organism = 'hsa',
                          pvalueCutoff = 0.05,
                          qvalueCutoff = 0.20) 

> head(summary(kegg_enrich))
[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust    qvalue      geneID      Count      
<0 rows> (or 0-length row.names)
Warning message:
In summary(kegg_enrich): summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.

> length(results_sig_entrez$entrez)
[1] 3640

When I look at the enrichResults object I can see that it has data within it. When I view the object there are 325 rows and 9 columns, however, when I try and display the results it does not show up with any data.

I get the same result when I use the the head(as.data.frame(kegg_enrich)) as well. It still shows no rows. If anyone has any insights on how to address this problem that would be much appreciated.

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

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

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

other attached packages:
 [1] pathview_1.26.0             ggsci_2.9                   gage_2.36.0                 dplyr_1.0.2                 topGO_2.38.1               
 [6] SparseM_1.78                graph_1.64.0                GO.db_3.10.0                RColorBrewer_1.1-2          genefilter_1.68.0          
[11] pheatmap_1.0.12             org.Hs.eg.db_3.10.0         org.Mm.eg.db_3.10.0         KEGG.db_3.2.3               AnnotationDbi_1.48.0       
[16] DOSE_3.12.0                 ReactomePA_1.30.0           biomaRt_2.42.1              clusterProfiler_3.14.3      EnhancedVolcano_1.4.0      
[21] ggrepel_0.9.0               ggplot2_3.3.3               DESeq2_1.26.0               SummarizedExperiment_1.16.1 DelayedArray_0.12.3        
[26] BiocParallel_1.20.1         matrixStats_0.57.0          Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.1        
[31] IRanges_2.20.2              S4Vectors_0.24.4            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
  [1] backports_1.2.0        Hmisc_4.4-2            fastmatch_1.1-0        BiocFileCache_1.10.2   plyr_1.8.6             igraph_1.2.6          
  [7] splines_3.6.1          urltools_1.7.3         digest_0.6.27          htmltools_0.5.0        GOSemSim_2.12.1        viridis_0.5.1         
 [13] magrittr_2.0.1         checkmate_2.0.0        memoise_1.1.0          cluster_2.1.0          Biostrings_2.54.0      annotate_1.64.0       
 [19] graphlayouts_0.7.1     askpass_1.1            enrichplot_1.6.1       prettyunits_1.1.1      jpeg_0.1-8.1           colorspace_2.0-0      
 [25] blob_1.2.1             rappdirs_0.3.1         xfun_0.19              crayon_1.3.4           RCurl_1.98-1.2         jsonlite_1.7.2        
 [31] survival_3.2-7         glue_1.4.2             polyclip_1.10-0        gtable_0.3.0           zlibbioc_1.32.0        XVector_0.26.0        
 [37] graphite_1.32.0        Rgraphviz_2.30.0       scales_1.1.1           DBI_1.1.0              Rcpp_1.0.5             viridisLite_0.3.0     
 [43] xtable_1.8-4           progress_1.2.2         htmlTable_2.1.0        gridGraphics_0.5-1     foreign_0.8-71         bit_4.0.4             
 [49] reactome.db_1.70.0     europepmc_0.4          Formula_1.2-4          htmlwidgets_1.5.3      httr_1.4.2             fgsea_1.12.0          
 [55] ellipsis_0.3.1         pkgconfig_2.0.3        XML_3.99-0.3           farver_2.0.3           nnet_7.3-12            dbplyr_2.0.0          
 [61] locfit_1.5-9.4         labeling_0.4.2         ggplotify_0.0.5        tidyselect_1.1.0       rlang_0.4.10           reshape2_1.4.4        
 [67] munsell_0.5.0          tools_3.6.1            generics_0.1.0         RSQLite_2.2.1          ggridges_0.5.2         stringr_1.4.0         
 [73] knitr_1.30             bit64_4.0.5            tidygraph_1.2.0        purrr_0.3.4            KEGGREST_1.26.1        ggraph_2.0.4          
 [79] KEGGgraph_1.46.0       DO.db_2.9              xml2_1.3.2             compiler_3.6.1         rstudioapi_0.13        curl_4.3              
 [85] png_0.1-7              tibble_3.0.4           tweenr_1.0.1           geneplotter_1.64.0     stringi_1.5.3          lattice_0.20-38       
 [91] Matrix_1.2-17          vctrs_0.3.6            pillar_1.4.7           lifecycle_0.2.0        BiocManager_1.30.10    triebeard_0.3.0       
 [97] data.table_1.13.6      cowplot_1.1.1          bitops_1.0-6           qvalue_2.18.0          R6_2.5.0               latticeExtra_0.6-29   
[103] gridExtra_2.3          MASS_7.3-51.4          assertthat_0.2.1       openssl_1.4.3          withr_2.3.0            GenomeInfoDbData_1.2.2
[109] hms_0.5.3              grid_3.6.1             rpart_4.1-15           tidyr_1.1.2            rvcheck_0.1.8          ggforce_0.3.2         
[115] base64enc_0.1-3

Answer 1

[halo22]

Are you sure that 'kegg_enrich' has the results? Try removing the filters and set it pvalueCutoff = 1 and qvalueCutoff =1. This is not the most ideal solution but should give you the data frame with results. In the past, the following has worked for me.

  kk <- enrichKEGG(gene = myGenes,
             organism     = 'hsa',
             pvalueCutoff = 1)
   kk <- as.data.frame(kk)

[geoffkerr22]

That solved it thanks! The cutoff's were too stringent.