clusterProfiler
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YuLab-SMU
富集分析时出现 no slot of name "dr" for this object of class "enrichResult"
For what it is worth: using the output of the code from the enrichGO help page, View is working fine for me in fresh sessions of both 'plain' R, and R-studio. I am using the latest versions of both.
> library(clusterProfiler)
> data(geneList, package = "DOSE")
> de <- names(geneList)[1:100]
>
> yy <- enrichGO(de, 'org.Hs.eg.db', ont="ALL", pvalueCutoff=0.01)
> head(yy)
ONTOLOGY ID Description GeneRatio BgRatio pvalue p.adjust
GO:0007059 BP GO:0007059 chromosome segregation 34/99 424/18870 2.432364e-31 3.996375e-28
GO:0098813 BP GO:0098813 nuclear chromosome segregation 30/99 312/18870 6.474483e-30 5.318788e-27
GO:0000819 BP GO:0000819 sister chromatid segregation 27/99 225/18870 1.557846e-29 8.531801e-27
GO:0000070 BP GO:0000070 mitotic sister chromatid segregation 25/99 184/18870 9.747875e-29 4.003940e-26
GO:0140014 BP GO:0140014 mitotic nuclear division 28/99 274/18870 1.225729e-28 4.027745e-26
GO:0000280 BP GO:0000280 nuclear division 32/99 441/18870 4.745944e-28 1.299598e-25
qvalue
GO:0007059 3.187677e-28
GO:0098813 4.242490e-27
GO:0000819 6.805326e-27
GO:0000070 3.193712e-26
GO:0140014 3.212700e-26
GO:0000280 1.036614e-25
geneID
GO:0007059 55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/55355/220134/51203/22974/10460/4751/79019/55839/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909/6790
GO:0098813 55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/51203/22974/10460/4751/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909/6790
GO:0000819 55143/991/9493/1062/4605/10403/7153/23397/9787/11065/51203/22974/10460/4751/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909
GO:0000070 55143/991/9493/1062/4605/10403/23397/9787/11065/51203/22974/4751/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909
GO:0140014 55143/991/9493/1062/4605/10403/23397/9787/11065/51203/22974/4751/27338/983/4085/81930/81620/332/3832/7272/64151/9212/1111/9319/9055/3833/146909/6790
GO:0000280 55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/51203/22974/4751/10635/27338/983/4085/81930/81620/332/3832/7272/64151/9212/1111/9319/9055/3833/146909/6790
Count
GO:0007059 34
GO:0098813 30
GO:0000819 27
GO:0000070 25
GO:0140014 28
GO:0000280 32
>
> View(yy)
>
> sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: Europe/Amsterdam
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_4.10.0
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7 magrittr_2.0.3
[5] farver_2.1.1 rmarkdown_2.25 fs_1.6.3 zlibbioc_1.48.0
[9] vctrs_0.6.4 memoise_2.0.1 DelayedMatrixStats_1.24.0 RCurl_1.98-1.13
[13] ggtree_3.10.0 htmltools_0.5.7 S4Arrays_1.2.0 curl_5.1.0
[17] AnnotationHub_3.10.0 SparseArray_1.2.2 gridGraphics_0.5-1 plyr_1.8.9
[21] cachem_1.0.8 igraph_1.5.1 mime_0.12 lifecycle_1.0.4
[25] pkgconfig_2.0.3 gson_0.1.0 rsvd_1.0.5 Matrix_1.6-3
[29] R6_2.5.1 fastmap_1.1.1 shiny_1.8.0 GenomeInfoDbData_1.2.11
[33] MatrixGenerics_1.14.0 digest_0.6.33 aplot_0.2.2 enrichplot_1.23.1
[37] colorspace_2.1-0 patchwork_1.1.3 AnnotationDbi_1.64.1 S4Vectors_0.40.2
[41] dqrng_0.3.2 irlba_2.3.5.1 RSQLite_2.3.3 org.Hs.eg.db_3.18.0
[45] beachmat_2.18.0 filelock_1.0.2 PCAtools_2.14.0 fansi_1.0.5
[49] httr_1.4.7 polyclip_1.10-6 abind_1.4-5 compiler_4.3.0
[53] bit64_4.0.5 withr_2.5.2 BiocParallel_1.36.0 viridis_0.6.4
[57] DBI_1.1.3 ggforce_0.4.1 MASS_7.3-60 rappdirs_0.3.3
[61] DelayedArray_0.28.0 HDO.db_0.99.1 tools_4.3.0 interactiveDisplayBase_1.40.0
[65] ape_5.7-1 scatterpie_0.2.1 httpuv_1.6.12 glue_1.6.2
[69] promises_1.2.1 nlme_3.1-164 GOSemSim_2.28.0 shadowtext_0.1.2
[73] grid_4.3.0 reshape2_1.4.4 fgsea_1.28.0 generics_0.1.3
[77] gtable_0.3.4 tidyr_1.3.0 data.table_1.14.8 BiocSingular_1.18.0
[81] tidygraph_1.2.3 ScaledMatrix_1.10.0 utf8_1.2.4 XVector_0.42.0
[85] BiocGenerics_0.48.1 BiocVersion_3.18.1 ggrepel_0.9.4 pillar_1.9.0
[89] stringr_1.5.1 yulab.utils_0.1.0 later_1.3.1 splines_4.3.0
[93] dplyr_1.1.4 tweenr_2.0.2 BiocFileCache_2.11.1 treeio_1.26.0
[97] lattice_0.22-5 bit_4.0.5 tidyselect_1.2.0 GO.db_3.18.0
[101] Biostrings_2.70.1 knitr_1.45 gridExtra_2.3 IRanges_2.36.0
[105] stats4_4.3.0 xfun_0.41 graphlayouts_1.0.2 Biobase_2.62.0
[109] matrixStats_1.1.0 stringi_1.8.2 VGAM_1.1-9 lazyeval_0.2.2
[113] ggfun_0.1.3 yaml_2.3.7 evaluate_0.23 codetools_0.2-19
[117] ggraph_2.1.0 tibble_3.2.1 qvalue_2.34.0 BiocManager_1.30.22
[121] ggplotify_0.1.2 cli_3.6.1 xtable_1.8-4 munsell_0.5.0
[125] Rcpp_1.0.11 GenomeInfoDb_1.38.1 dbplyr_2.4.0 png_0.1-8
[129] parallel_4.3.0 ellipsis_0.3.2 ggplot2_3.4.4 blob_1.2.4
[133] DOSE_3.28.1 sparseMatrixStats_1.14.0 bitops_1.0-7 viridisLite_0.4.2
[137] tidytree_0.4.5 scales_1.3.0 purrr_1.0.2 crayon_1.5.2
[141] rlang_1.1.2 cowplot_1.1.1 fastmatch_1.1-4 KEGGREST_1.42.0
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