clusterProfiler
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Published
20 hours ago •
YuLab-SMU
YuLab-SMU
enrichKEGG function error
hello author Thank you very much for developing such an excellent analysis tool. I encountered a problem when using the enrichKEGG function today. ”--> No gene can be mapped.... --> Expected input gene ID: --> return NULL..." I performed go enrichment analysis in the previous step of kegg analysis, and there is no problem with my gene list. And I had the same problem when running the examples data.
@wang0430 After updates as mentioned #549 and restarting R (v4.2.1), clusterProfiler (v.4.7.1.002, requires updates of DOSE (v.3.25.0.002) as well), enrichKEGG() is working fine (for me, it is human data).
~$ R
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(clusterProfiler)
clusterProfiler v4.7.1.002 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141
Attaching package: ‘clusterProfiler’
The following object is masked from ‘package:stats’:
filter
> data(geneList, package="DOSE")
> gene <- names(geneList)[abs(geneList) > 2]
kk <- enrichKEGG(gene = gene,
>
> kk <- enrichKEGG(gene = gene,
+ organism = 'hsa',
+ pvalueCutoff = 0.05)
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
> head(kk)
ID Description
hsa04110 hsa04110 Cell cycle
hsa04114 hsa04114 Oocyte meiosis
hsa04218 hsa04218 Cellular senescence
hsa04061 hsa04061 Viral protein interaction with cytokine and cytokine receptor
hsa03320 hsa03320 PPAR signaling pathway
hsa04914 hsa04914 Progesterone-mediated oocyte maturation
GeneRatio BgRatio pvalue p.adjust qvalue
hsa04110 11/94 127/8275 1.689644e-07 3.531357e-05 3.450432e-05
hsa04114 10/94 131/8275 2.051606e-06 2.143928e-04 2.094797e-04
hsa04218 10/94 156/8275 9.875269e-06 6.879771e-04 6.722113e-04
hsa04061 8/94 100/8275 1.622516e-05 8.477647e-04 8.283372e-04
hsa03320 7/94 75/8275 2.061911e-05 8.618789e-04 8.421279e-04
hsa04914 7/94 102/8275 1.496049e-04 5.211236e-03 5.091815e-03
geneID Count
hsa04110 8318/991/9133/890/983/4085/7272/1111/891/4174/9232 11
hsa04114 991/9133/983/4085/51806/6790/891/9232/3708/5241 10
hsa04218 2305/4605/9133/890/983/51806/1111/891/776/3708 10
hsa04061 3627/10563/6373/4283/6362/6355/9547/1524 8
hsa03320 4312/9415/9370/5105/2167/3158/5346 7
hsa04914 9133/890/983/4085/6790/891/5241 7
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=sv_SE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=sv_SE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=sv_SE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_4.7.1.002
loaded via a namespace (and not attached):
[1] nlme_3.1-159 bitops_1.0-7 ggtree_3.6.2
[4] enrichplot_1.18.3 bit64_4.0.5 HDO.db_0.99.1
[7] RColorBrewer_1.1-3 httr_1.4.5 GenomeInfoDb_1.34.9
[10] tools_4.2.1 utf8_1.2.3 R6_2.5.1
[13] lazyeval_0.2.2 DBI_1.1.3 BiocGenerics_0.44.0
[16] colorspace_2.1-0 withr_2.5.0 tidyselect_1.2.0
[19] gridExtra_2.3 bit_4.0.5 compiler_4.2.1
[22] cli_3.6.0 Biobase_2.58.0 scatterpie_0.1.8
[25] shadowtext_0.1.2 scales_1.2.1 stringr_1.5.0
[28] digest_0.6.31 yulab.utils_0.0.6 gson_0.1.0
[31] DOSE_3.25.0.002 XVector_0.38.0 pkgconfig_2.0.3
[34] fastmap_1.1.1 rlang_1.0.6 RSQLite_2.3.0
[37] gridGraphics_0.5-1 farver_2.1.1 generics_0.1.3
[40] jsonlite_1.8.4 BiocParallel_1.32.5 GOSemSim_2.24.0
[43] dplyr_1.1.0 RCurl_1.98-1.10 magrittr_2.0.3
[46] ggplotify_0.1.0 GO.db_3.16.0 GenomeInfoDbData_1.2.9
[49] patchwork_1.1.2 Matrix_1.5-1 Rcpp_1.0.10
[52] munsell_0.5.0 S4Vectors_0.36.2 fansi_1.0.4
[55] ape_5.7 viridis_0.6.2 lifecycle_1.0.3
[58] stringi_1.7.12 ggraph_2.1.0 MASS_7.3-58.1
[61] zlibbioc_1.44.0 plyr_1.8.8 qvalue_2.30.0
[64] grid_4.2.1 blob_1.2.3 parallel_4.2.1
[67] ggrepel_0.9.3 crayon_1.5.2 lattice_0.20-45
[70] graphlayouts_0.8.4 Biostrings_2.66.0 cowplot_1.1.1
[73] splines_4.2.1 KEGGREST_1.38.0 pillar_1.8.1
[76] fgsea_1.24.0 igraph_1.4.1 reshape2_1.4.4
[79] codetools_0.2-18 stats4_4.2.1 fastmatch_1.1-3
[82] glue_1.6.2 ggfun_0.0.9 downloader_0.4
[85] data.table_1.14.8 treeio_1.22.0 png_0.1-8
[88] vctrs_0.5.2 tweenr_2.0.2 gtable_0.3.1
[91] purrr_1.0.1 polyclip_1.10-4 tidyr_1.3.0
[94] cachem_1.0.7 ggplot2_3.4.1 ggforce_0.4.1
[97] tidygraph_1.2.3 tidytree_0.4.2 viridisLite_0.4.1
[100] tibble_3.1.8 aplot_0.1.9 AnnotationDbi_1.60.0
[103] memoise_2.0.1 IRanges_2.32.0
I think something has changed on KEGG's end such that older versions of clusterprofiler are not accurately pulling data from KEGG, that's my best guess any way cuz I'm re-running some code with clusterProfiler 3.18.1 and I'm now getting the same error, but it worked fine when i first put the code together back in late 2021.
