The items in "Description" column by enrichKEGG are all "NA" #806
Description
I met this problem when I run enrichKEGG recently, I know that setting "use_internal_data = F" will allow it to run normally, but sometimes the network is bad, and I need to run it offline.
library(clusterProfiler)
> data(geneList, package='DOSE')
> de <- names(geneList)[1:100]
> kegg_out <- enrichKEGG(de,
organism= 'hsa',
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
#qvalueCutoff = 0.05,
use_internal_data = T
)
> head(kegg_out@result)
category subcategory ID Description GeneRatio
hsa04110 Cellular Processes Cell growth and death hsa04110 <NA> 8/47
hsa04218 Cellular Processes Cell growth and death hsa04218 <NA> 7/47
hsa04114 Cellular Processes Cell growth and death hsa04114 <NA> 6/47
hsa04657 Organismal Systems Immune system hsa04657 <NA> 5/47
hsa04061 Environmental Information Processing Signaling molecules and interaction hsa04061 <NA> 5/47
hsa04914 Organismal Systems Endocrine system hsa04914 <NA> 5/47
BgRatio pvalue p.adjust qvalue geneID Count
hsa04110 126/8146 4.971666e-07 5.965999e-05 5.442666e-05 8318/991/9133/890/983/4085/7272/1111 8
hsa04218 156/8146 2.729247e-05 1.637548e-03 1.493904e-03 2305/4605/9133/890/983/51806/1111 7
hsa04114 131/8146 9.641884e-05 3.856753e-03 3.518442e-03 991/9133/983/4085/51806/6790 6
hsa04657 94/8146 1.922807e-04 5.638090e-03 5.143521e-03 4312/6280/6279/6278/3627 5
hsa04061 100/8146 2.570139e-04 5.638090e-03 5.143521e-03 3627/10563/6373/4283/6362 5
hsa04914 102/8146 2.819045e-04 5.638090e-03 5.143521e-03 9133/890/983/4085/6790 5
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_4.18.4
loaded via a namespace (and not attached):
[1] fgsea_1.24.0 colorspace_2.1-2 ggtree_3.6.2 gson_0.1.0
[5] qvalue_2.30.0 XVector_0.38.0 fs_1.6.6 aplot_0.2.9
[9] dichromat_2.0-0.1 rstudioapi_0.18.0 farver_2.1.2 graphlayouts_1.2.2
[13] ggrepel_0.9.6 bit64_4.6.0-1 AnnotationDbi_1.60.2 scatterpie_0.2.6
[17] KEGG.db_2.8.0 codetools_0.2-20 splines_4.2.0 R.methodsS3_1.8.2
[21] cachem_1.1.0 GOSemSim_2.31.2 polyclip_1.10-7 jsonlite_2.0.0
[25] GO.db_3.16.0 png_0.1-8 R.oo_1.27.1 ggforce_0.5.0
[29] compiler_4.2.0 httr_1.4.7 enrichit_0.1.0 Matrix_1.6-2
[33] fastmap_1.2.0 lazyeval_0.2.2 cli_3.6.5 tweenr_2.0.3
[37] htmltools_0.5.9 tools_4.2.0 igraph_2.2.1 gtable_0.3.6
[41] glue_1.8.0 GenomeInfoDbData_1.2.9 reshape2_1.4.5 dplyr_1.1.4
[45] rappdirs_0.3.4 fastmatch_1.1-8 Rcpp_1.1.1 enrichplot_1.18.4
[49] Biobase_2.58.0 fontquiver_0.2.1 vctrs_0.7.0 Biostrings_2.66.0
[53] ape_5.8-1 nlme_3.1-168 ggraph_2.2.2 stringr_1.6.0
[57] lifecycle_1.0.5 DOSE_3.24.2 zlibbioc_1.44.0 MASS_7.3-60
[61] scales_1.4.0 tidygraph_1.3.1 parallel_4.2.0 fontLiberation_0.1.0
[65] RColorBrewer_1.1-3 memoise_2.0.1 gridExtra_2.3 ggplot2_4.0.1
[69] ggfun_0.2.0 HDO.db_0.99.1 gdtools_0.4.4 yulab.utils_0.2.3
[73] stringi_1.8.7 RSQLite_2.4.5 fontBitstreamVera_0.1.1 S4Vectors_0.36.2
[77] tidytree_0.4.7 BiocGenerics_0.44.0 BiocParallel_1.32.6 GenomeInfoDb_1.34.9
[81] rlang_1.1.7 pkgconfig_2.0.3 systemfonts_1.3.1 bitops_1.0-9
[85] ggiraph_0.9.3 lattice_0.22-7 purrr_1.2.1 treeio_1.22.0
[89] patchwork_1.3.2 htmlwidgets_1.6.4 cowplot_1.2.0 shadowtext_0.1.6
[93] bit_4.6.0 tidyselect_1.2.1 plyr_1.8.9 magrittr_2.0.4
[97] R6_2.6.1 IRanges_2.32.0 generics_0.1.4 DBI_1.2.3
[101] pillar_1.11.1 withr_3.0.2 KEGGREST_1.50.0 RCurl_1.98-1.17
[105] tibble_3.3.1 crayon_1.5.3 viridis_0.6.5 grid_4.2.0
[109] data.table_1.18.0 blob_1.3.0 S7_0.2.1 digest_0.6.39
[113] tidyr_1.3.2 gridGraphics_0.5-1 R.utils_2.13.0 stats4_4.2.0
[117] viridisLite_0.4.2 ggplotify_0.1.3