groupGO函数运行失败

[jiangzhichao47-create]

我在运行groupGO函数时会出现这种情况，如何在函数定义时用这种方式DOSE:::TERMID2EXTID使用DOSE包相关函数则运行结果正常

[guidohooiveld]

I don't understand; what is the exact use case or error you have?

I am asking because your code seems to work in my hands.... Note that I obtained the same GO category as in your screenshot.

> library(clusterProfiler)
> library(DOSE)
> library(org.Hs.eg.db)
> 
> data(geneList)
> gene <- names(geneList)[abs(geneList) > 2]
> ggo_level_1 <- groupGO(gene = gene,
+                        OrgDb = org.Hs.eg.db,
+                        ont="MF",
+                        level=1,
+                        readable=TRUE)
>
> ggo_level_1
GO MF Profiles at level 1 of 207 Homo sapiens genes 
> head(ggo_level_1)
                   ID        Description Count GeneRatio
GO:0003674 GO:0003674 molecular_function   195   195/207
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       geneID
GO:0003674 MMP1/CDC45/NMU/CDCA8/MCM10/CDC20/S100A9/FOXM1/KIF23/CENPE/KRT16/MYBL2/MELK/CCNB2/S100A8/NDC80/MARCO/BCL2A1/TOP2A/NCAPH/S100A7/E2F8/ASPM/CRABP1/CXCL10/RRM2/CEP55/DLGAP5/UGT8/UBE2C/HJURP/APOBEC3B/SKA1/PBK/NUSAP1/ISG20/CDCA3/TPX2/TACC3/CXCL13/NEK2/CXCL11/SLC7A5/CAMP/RAD51AP1/DUSP2/CXCL9/ADAMDEC1/CENPN/UBE2S/CCNA2/FADS2/CDK1/ERCC6L/MSLN/MAD2L1/CCL18/GINS1/PAX6/IL1R2/KIF18A/RARRES1/CDT1/BIRC5/INAVA/PGBD5/KIF11/S100P/PDK1/EZH2/GZMB/TRAT1/TTK/GABRP/NCAPG/CALML5/AQP9/GPR19/AURKB/CHODL/GINS2/NOL4/NRTN/CHAF1B/CHEK1/TRIP13/PRC1/KIFC1/KIF18B/QPRT/MMP12/SLC2A6/KIF20A/LAG3/IDO1/KRT81/DTL/AURKA/NUDT1/CCNB1/PLAAT1/PIR/CSN3/KIF4A/CCL8/GNLY/MCM5/PTTG1/COL16A1/CACNA1D/MAOB/ADIPOQ/VSTM4/MYRIP/FCGBP/DACH1/ITPR1/ZNF423/RAI2/SYT17/SLC16A4/CORIN/ANXA9/KCNK15/MMP28/IQCH/MYH11/AK5/RNASE4/CA12/KCNE4/HLA-DQA1/CCDC170/TBC1D9/ADH1B/NOVA1/COMP/PCK1/PDZK1/EMX2/C1orf21/ACKR1/COL17A1/SCGB2A2/PSD3/FABP4/EMCN/GAMT/BMP4/SLC44A4/LRP2/NLGN4X/PPP1R3C/DNAJC12/ABLIM3/MAPT/CILP/CCN5/ERBB4/NDP/MATN3/MLPH/CHAD/HMGCS2/FOXA1/PLIN1/CRY2/CXCL14/GRP/CYP4F8/TPSB2/ASPN/CX3CR1/LRRC17/CYP4B1/TRIM58/ABCA8/FMO5/PIP/STC2/GATA3/TFAP2B/DNALI1/STEAP4/PTPRT/STK32B/NAT1/MFAP4/PGR/AGR2/ADIRF/TMC5/CYBRD1/SCUBE2/OGN
> 
> 
> packageVersion("clusterProfiler")
[1] ‘4.18.4’
> packageVersion("org.Hs.eg.db")
[1] ‘3.22.0’
> 
> sessionInfo()
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Europe/Amsterdam
tzcode source: internal

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

other attached packages:
[1] DOSE_4.4.0             org.Hs.eg.db_3.22.0    AnnotationDbi_1.72.0  
[4] IRanges_2.44.0         S4Vectors_0.48.0       Biobase_2.70.0        
[7] BiocGenerics_0.56.0    generics_0.1.4         clusterProfiler_4.18.4

loaded via a namespace (and not attached):
 [1] DBI_1.3.0               gson_0.1.0              rlang_1.1.7            
 [4] magrittr_2.0.4          otel_0.2.0              compiler_4.5.1         
 [7] RSQLite_2.4.6           png_0.1-9               systemfonts_1.3.2      
[10] vctrs_0.7.1             reshape2_1.4.5          stringr_1.6.0          
[13] pkgconfig_2.0.3         crayon_1.5.3            fastmap_1.2.0          
[16] XVector_0.50.0          enrichplot_1.30.5       purrr_1.2.1            
[19] bit_4.6.0               cachem_1.1.0            aplot_0.2.9            
[22] jsonlite_2.0.0          blob_1.3.0              tidydr_0.0.6           
[25] BiocParallel_1.44.0     tweenr_2.0.3            parallel_4.5.1         
[28] cluster_2.1.8.2         R6_2.6.1                stringi_1.8.7          
[31] RColorBrewer_1.1-3      GOSemSim_2.36.0         Rcpp_1.1.1             
[34] Seqinfo_1.0.0           ggtangle_0.1.1          R.utils_2.13.0         
[37] Matrix_1.7-4            splines_4.5.1           igraph_2.2.2           
[40] tidyselect_1.2.1        qvalue_2.42.0           dichromat_2.0-0.1      
[43] codetools_0.2-20        lattice_0.22-9          tibble_3.3.1           
[46] plyr_1.8.9              treeio_1.34.0           withr_3.0.2            
[49] KEGGREST_1.50.0         S7_0.2.1                gridGraphics_0.5-1     
[52] scatterpie_0.2.6        polyclip_1.10-7         Biostrings_2.78.0      
[55] pillar_1.11.1           ggtree_4.0.4            ggfun_0.2.0            
[58] ggplot2_4.0.2           scales_1.4.0            tidytree_0.4.7         
[61] glue_1.8.0              gdtools_0.5.0           lazyeval_0.2.2         
[64] tools_4.5.1             ggnewscale_0.5.2        data.table_1.18.2.1    
[67] fgsea_1.36.2            ggiraph_0.9.6           fs_1.6.7               
[70] fastmatch_1.1-8         cowplot_1.2.0           grid_4.5.1             
[73] tidyr_1.3.2             ape_5.8-1               nlme_3.1-168           
[76] patchwork_1.3.2         ggforce_0.5.0           cli_3.6.5              
[79] rappdirs_0.3.4          fontBitstreamVera_0.1.1 dplyr_1.2.0            
[82] gtable_0.3.6            R.methodsS3_1.8.2       yulab.utils_0.2.4      
[85] digest_0.6.39           fontquiver_0.2.1        ggrepel_0.9.8          
[88] ggplotify_0.1.3         htmlwidgets_1.6.4       farver_2.1.2           
[91] memoise_2.0.1           htmltools_0.5.9         R.oo_1.27.1            
[94] lifecycle_1.0.5         httr_1.4.8              GO.db_3.22.0           
[97] fontLiberation_0.1.0    bit64_4.6.0-1           MASS_7.3-65            
> 
> 
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