enricher报错在进行非模式生物的KEGG富集分析

[Tsebifera]

我可以使用enricherGO进行GO分析，但是当我使用enricher进行KEGG富集分析会报错： KEGG <- enricher(genes, TERM2GENE = gene2pathway, TERM2NAME = pathway2name,gson = NULL, pvalueCutoff = 0.05, qvalueCutoff = 0.05, # pAdjustMethod = "BH", minGSSize = 1)#基因集的最小基因数，最小最大默认是[10,500]，在富集不显著时设置。 Rstudio报错如下--> No gene can be mapped....--> Expected input gene ID: ko02000--> return NULL... 我的格式是对标enricher要求的genes也是向量。 我尝试了github中所提及的解决方案并且调高了 pvalueCutoff, qvalueCutoff ： devtools::install_github("YuLab-SMU/DOSE") devtools::install_github("YuLab-SMU/HDO.db") devtools::install_github('YuLab-SMU/clusterProfiler') 。并没有用还是报错。我要富集的转录本的KEGG和背景的是有重叠的，并不是空集。

[Tsebifera]

sessionInfo() R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Tokyo tzcode source: internal

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

other attached packages: [1] clusterProfiler_4.11.0 ontologyIndex_2.11 jsonlite_1.8.7 stringr_1.5.0
[5] dplyr_1.1.3

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 magrittr_2.0.3
[4] farver_2.1.1 fs_1.6.3 zlibbioc_1.48.0
[7] vctrs_0.6.4 memoise_2.0.1 RCurl_1.98-1.12
[10] ggtree_3.8.2 usethis_2.2.2 htmltools_0.5.6.1
[13] AnnotationHub_3.10.0 curl_5.1.0 gridGraphics_0.5-1
[16] desc_1.4.2 htmlwidgets_1.6.2 plyr_1.8.9
[19] cachem_1.0.8 rio_1.0.1 igraph_1.5.1
[22] mime_0.12 lifecycle_1.0.3 pkgconfig_2.0.3
[25] gson_0.1.0 Matrix_1.6-1.1 R6_2.5.1
[28] fastmap_1.1.1 GenomeInfoDbData_1.2.11 shiny_1.7.5.1
[31] digest_0.6.33 aplot_0.2.1 enrichplot_1.20.3
[34] colorspace_2.1-0 ps_1.7.5 patchwork_1.1.3
[37] AnnotationDbi_1.64.0 S4Vectors_0.40.1 rprojroot_2.0.3
[40] pkgload_1.3.3 RSQLite_2.3.2 MPO.db_0.99.7
[43] filelock_1.0.2 fansi_1.0.5 httr_1.4.7
[46] polyclip_1.10-6 HPO.db_0.99.2 compiler_4.3.1
[49] remotes_2.4.2.1 bit64_4.0.5 withr_2.5.1
[52] BiocParallel_1.36.0 viridis_0.6.4 DBI_1.1.3
[55] pkgbuild_1.4.2 ggforce_0.4.1 R.utils_2.12.2
[58] MASS_7.3-60 sessioninfo_1.2.2 rappdirs_0.3.3
[61] HDO.db_0.99.1 tools_4.3.1 ape_5.7-1
[64] scatterpie_0.2.1 interactiveDisplayBase_1.40.0 httpuv_1.6.12
[67] R.oo_1.25.0 glue_1.6.2 callr_3.7.3
[70] nlme_3.1-163 GOSemSim_2.28.0 promises_1.2.1
[73] grid_4.3.1 shadowtext_0.1.2 reshape2_1.4.4
[76] fgsea_1.28.0 generics_0.1.3 gtable_0.3.4
[79] R.methodsS3_1.8.2 tidyr_1.3.0 data.table_1.14.8
[82] tidygraph_1.2.3 utf8_1.2.4 XVector_0.42.0
[85] BiocGenerics_0.48.0 ggrepel_0.9.3 BiocVersion_3.18.0
[88] pillar_1.9.0 yulab.utils_0.1.0 later_1.3.1
[91] splines_4.3.1 tweenr_2.0.2 BiocFileCache_2.10.1
[94] treeio_1.24.3 lattice_0.21-9 bit_4.0.5
[97] tidyselect_1.2.0 GO.db_3.18.0 miniUI_0.1.1.1
[100] Biostrings_2.70.1 gridExtra_2.3 IRanges_2.36.0
[103] stats4_4.3.1 graphlayouts_1.0.1 Biobase_2.62.0
[106] devtools_2.4.5 stringi_1.7.12 lazyeval_0.2.2
[109] ggfun_0.1.3 yaml_2.3.7 codetools_0.2-19
[112] ggraph_2.1.0 tibble_3.2.1 qvalue_2.34.0
[115] BiocManager_1.30.22 ggplotify_0.1.2 cli_3.6.1
[118] xtable_1.8-4 processx_3.8.2 munsell_0.5.0
[121] Rcpp_1.0.11 GenomeInfoDb_1.38.0 dbplyr_2.4.0
[124] png_0.1-8 parallel_4.3.1 ellipsis_0.3.2
[127] ggplot2_3.4.4 blob_1.2.4 prettyunits_1.2.0
[130] profvis_0.3.8 DOSE_3.29.0 urlchecker_1.0.1
[133] bitops_1.0-7 viridisLite_0.4.2 tidytree_0.4.5
[136] scales_1.2.1 purrr_1.0.2 crayon_1.5.2
[139] rlang_1.1.1 cowplot_1.1.1 fastmatch_1.1-4
[142] KEGGREST_1.42.0

[huerqiang]

从报错信息来看就是你输入的基因与TERM2GENE的基因id不同，请仔细检查一下。