enrichkegg函数报错

[PanSX-Dr]

于老师，我最近在用clusterprofiler进行kegg分析，运行enrichkegg函数的时候代码如下：kk <- enrichKEGG(gene = gene, organism = 'hsa', pvalueCutoff = 0.05)，但是提示报错信息如下：Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"... Error in file(con, "r") : cannot open the connection to 'https://rest.kegg.jp/link/hsa/pathway' 此外: Warning message: In file(con, "r") : URL 'https://rest.kegg.jp/link/hsa/pathway': status was 'SSL connect error'。尝试过很多问题，请问这个该怎么结局。

[huerqiang]

你这个是网络问题，尝试换别的网络，并且安装最新版本的clusterProfiler后再试试吧，

[PanSX-Dr]

您好老师，我的clusterprofiler应该是最新版本的。一直不行，然后尝试了在本地运行enrichkegg，代码如下 kk <- enrichKEGG(gene = gene, organism = 'hsa', pvalueCutoff = 0.05, use_internal_data = T) 然后能够运行出来结果，但是富集的结果和您的教程里不一样，我腹肌的结果如下 在discription那一列只显示的kegg的编号，但是在教程里面应该是具体的某个信号通路的描述。而且我本地运行的还多出来了category和subcategory两列。请问这是什么原因呢？ sessionInfo() R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 [2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai tzcode source: internal

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

other attached packages: [1] clusterProfiler_4.10.0

loaded via a namespace (and not attached): [1] IRanges_2.36.0 nnet_7.3-19
[3] goftest_1.2-3 Biostrings_2.70.2
[5] vctrs_0.6.5 spatstat.random_3.2-2
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[9] shape_1.4.6 ggrepel_0.9.5
[11] deldir_2.0-2 parallelly_1.36.0
[13] MASS_7.3-60.0.1 reshape2_1.4.4
[15] httpuv_1.6.14 foreach_1.5.2
[17] BiocGenerics_0.48.1 qvalue_2.34.0
[19] withr_3.0.0 ggfun_0.1.4
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[23] memoise_2.0.1 gson_0.1.0
[25] tidyHeatmap_1.8.1 tidytree_0.4.6
[27] zoo_1.8-12 GlobalOptions_0.1.2
[29] DNAcopy_1.76.0 pbapply_1.7-2
[31] KEGGREST_1.42.0 promises_1.2.1
[33] httr_1.4.7 globals_0.16.2
[35] fitdistrplus_1.1-11 rstudioapi_0.15.0
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[45] polyclip_1.10-6 GenomeInfoDbData_1.2.11
[47] SparseArray_1.2.3 interactiveDisplayBase_1.40.0 [49] xtable_1.8-4 stringr_1.5.1
[51] doParallel_1.0.17 S4Arrays_1.2.0
[53] BiocFileCache_2.10.1 hms_1.1.3
[55] glmnet_4.1-8 GenomicRanges_1.54.1
[57] irlba_2.3.5.1 colorspace_2.1-0
[59] filelock_1.0.3 ROCR_1.0-11
[61] reticulate_1.35.0 spatstat.data_3.0-4
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[65] readr_2.1.5 later_1.3.2
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[71] future.apply_1.11.1 scattermore_1.2
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[75] cowplot_1.1.3 matrixStats_1.2.0
[77] RcppAnnoy_0.0.22 pillar_1.9.0
[79] nlme_3.1-164 iterators_1.0.14
[81] compiler_4.3.2 RSpectra_0.16-1
[83] stringi_1.8.3 UCSCXenaTools_1.4.8
[85] jomo_2.7-6 tensor_1.5
[87] minqa_1.2.6 SummarizedExperiment_1.32.0
[89] dendextend_1.17.1 lubridate_1.9.3
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[105] mime_0.12 splines_4.3.2
[107] circlize_0.4.15 Rcpp_1.0.12
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[125] tweenr_2.0.2 pkgconfig_2.0.3
[127] tools_4.3.2 cachem_1.0.8
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[179] lazyeval_0.2.2 shiny_1.8.0
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