BaymaxzzZY
commented
1 year ago 2023/06/27
Open BaymaxzzZY opened 1 year ago
BaymaxzzZY
commented
1 year ago 2023/06/27
alessandriLuca
commented
1 year ago Im having the same issue, im working in a docker environment, with ubuntu, someone fixed this problem changing the download method using wget, but noone of the methods worked for me. IS there a way to download manually and give the local path?
guidohooiveld
commented
1 year ago FWIW: the example code is working in my hands...
> library(clusterProfiler)
> data(geneList, package="DOSE")
> gene <- names(geneList)[abs(geneList) > 2]
>
> kk <- enrichKEGG(gene = gene,
+ organism = 'hsa',
+ pvalueCutoff = 0.05)
> 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
hsa04814 hsa04814 Motor proteins
GeneRatio BgRatio pvalue p.adjust qvalue
hsa04110 15/106 157/8577 6.842507e-10 1.443769e-07 1.426123e-07
hsa04114 10/106 131/8577 4.501085e-06 4.748645e-04 4.690604e-04
hsa04218 10/106 156/8577 2.116198e-05 1.488392e-03 1.470200e-03
hsa04061 8/106 100/8577 3.031883e-05 1.515949e-03 1.497420e-03
hsa03320 7/106 75/8577 3.592296e-05 1.515949e-03 1.497420e-03
hsa04814 10/106 193/8577 1.288529e-04 4.531326e-03 4.475942e-03
geneID
hsa04110 8318/991/9133/10403/890/983/4085/81620/7272/9212/1111/9319/891/4174/9232
hsa04114 991/9133/983/4085/51806/6790/891/9232/3708/5241
hsa04218 2305/4605/9133/890/983/51806/1111/891/776/3708
hsa04061 3627/10563/6373/4283/6362/6355/9547/1524
hsa03320 4312/9415/9370/5105/2167/3158/5346
hsa04814 9493/1062/81930/3832/3833/146909/10112/24137/4629/7802
Count
hsa04110 15
hsa04114 10
hsa04218 10
hsa04061 8
hsa03320 7
hsa04814 10
>
> packageVersion("clusterProfiler")
[1] ‘4.8.2’
>
> 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
[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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_4.8.2
loaded via a namespace (and not attached):
[1] DBI_1.1.3 bitops_1.0-7 gson_0.1.0
[4] shadowtext_0.1.2 gridExtra_2.3 rlang_1.1.1
[7] magrittr_2.0.3 DOSE_3.26.1 compiler_4.3.0
[10] RSQLite_2.3.1 png_0.1-8 vctrs_0.6.3
[13] reshape2_1.4.4 stringr_1.5.0 pkgconfig_2.0.3
[16] crayon_1.5.2 fastmap_1.1.1 XVector_0.40.0
[19] ggraph_2.1.0 utf8_1.2.3 HDO.db_0.99.1
[22] enrichplot_1.20.0 purrr_1.0.1 bit_4.0.5
[25] zlibbioc_1.46.0 cachem_1.0.8 aplot_0.1.10
[28] GenomeInfoDb_1.36.1 jsonlite_1.8.7 blob_1.2.4
[31] BiocParallel_1.34.2 tweenr_2.0.2 parallel_4.3.0
[34] R6_2.5.1 stringi_1.7.12 RColorBrewer_1.1-3
[37] GOSemSim_2.26.1 Rcpp_1.0.11 downloader_0.4
[40] IRanges_2.34.1 Matrix_1.6-0 splines_4.3.0
[43] igraph_1.5.0 tidyselect_1.2.0 qvalue_2.32.0
[46] viridis_0.6.3 codetools_0.2-19 lattice_0.21-8
[49] tibble_3.2.1 plyr_1.8.8 Biobase_2.60.0
[52] treeio_1.24.2 withr_2.5.0 KEGGREST_1.40.0
[55] gridGraphics_0.5-1 scatterpie_0.2.1 polyclip_1.10-4
[58] Biostrings_2.68.1 BiocManager_1.30.21.1 pillar_1.9.0
[61] ggtree_3.8.0 stats4_4.3.0 ggfun_0.1.1
[64] generics_0.1.3 RCurl_1.98-1.12 S4Vectors_0.38.1
[67] ggplot2_3.4.2 munsell_0.5.0 scales_1.2.1
[70] tidytree_0.4.4 glue_1.6.2 lazyeval_0.2.2
[73] tools_4.3.0 data.table_1.14.8 fgsea_1.26.0
[76] graphlayouts_1.0.0 fastmatch_1.1-3 tidygraph_1.2.3
[79] cowplot_1.1.1 grid_4.3.0 tidyr_1.3.0
[82] ape_5.7-1 AnnotationDbi_1.62.2 colorspace_2.1-0
[85] nlme_3.1-162 GenomeInfoDbData_1.2.10 patchwork_1.1.2
[88] ggforce_0.4.1 cli_3.6.1 fansi_1.0.4
[91] viridisLite_0.4.2 dplyr_1.1.2 gtable_0.3.3
[94] yulab.utils_0.0.6 digest_0.6.33 BiocGenerics_0.46.0
[97] ggrepel_0.9.3 ggplotify_0.1.1 farver_2.1.1
[100] memoise_2.0.1 lifecycle_1.0.3 httr_1.4.6
[103] GO.db_3.17.0 bit64_4.0.5 MASS_7.3-60
>
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] grid stats4 stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] DOSE_3.26.1 org.Hs.eg.db_3.17.0 AnnotationDbi_1.62.1 [4] IRanges_2.34.1 S4Vectors_0.38.1 clusterProfiler_4.8.1 [7] edgeR_3.42.4 limma_3.56.2 missForest_1.5
[10] mice_3.16.0 rrcovNA_0.5-0 rrcov_1.7-4
[13] robustbase_0.99-0 VIM_6.2.2 colorspace_2.1-0
[16] imputeLCMD_2.1 tmvtnorm_1.5 gmm_1.8
[19] sandwich_3.0-2 mvtnorm_1.2-2 norm_1.0-11.1
[22] pcaMethods_1.92.0 impute_1.74.1 e1071_1.7-13
[25] Amelia_1.8.1 Rcpp_1.0.10 cowplot_1.1.1
[28] ggExtra_0.10.0 vegan_2.6-4 lattice_0.21-8
[31] permute_0.9-7 Metrics_0.1.4 raster_3.6-20
[34] sp_2.0-0 openxlsx_4.2.5.2 ggsci_3.0.0
[37] reshape2_1.4.4 glmnet_4.1-7 Matrix_1.5-4.1
[40] gdata_2.19.0 DT_0.28 shinyWidgets_0.7.6
[43] shinyjs_2.1.0 shinyBS_0.61.1 shiny_1.7.4
[46] devtools_2.4.5 usethis_2.2.1 data.table_1.14.8
[49] magrittr_2.0.3 lubridate_1.9.2 forcats_1.0.0
[52] stringr_1.5.0 dplyr_1.1.2 purrr_1.0.1
[55] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[58] ggplot2_3.4.2 tidyverse_2.0.0 Biobase_2.60.0
[61] BiocGenerics_0.46.0
loaded via a namespace (and not attached): [1] fs_1.6.2 bitops_1.0-7 enrichplot_1.20.0
[4] RColorBrewer_1.1-3 HDO.db_0.99.1 httr_1.4.6
[7] profvis_0.3.8 tools_4.3.1 doRNG_1.8.6
[10] backports_1.4.1 utf8_1.2.3 R6_2.5.1
[13] lazyeval_0.2.2 mgcv_1.8-42 jomo_2.7-6
[16] urlchecker_1.0.1 withr_2.5.0 gridExtra_2.3
[19] prettyunits_1.1.1 cli_3.6.1 pacman_0.5.1
[22] scatterpie_0.2.1 sass_0.4.6 randomForest_4.7-1.1
[25] proxy_0.4-27 yulab.utils_0.0.6 gson_0.1.0
[28] foreign_0.8-84 R.utils_2.12.2 sessioninfo_1.2.2
[31] itertools_0.1-3 rstudioapi_0.14 RSQLite_2.3.1
[34] gridGraphics_0.5-1 generics_0.1.3 shape_1.4.6
[37] gtools_3.9.4 car_3.1-2 zip_2.3.0
[40] GO.db_3.17.0 fansi_1.0.4 abind_1.4-5
[43] R.methodsS3_1.8.2 terra_1.7-39 lifecycle_1.0.3
[46] carData_3.0-5 qvalue_2.32.0 blob_1.2.4
[49] promises_1.2.0.1 crayon_1.5.2 mitml_0.4-5
[52] miniUI_0.1.1.1 KEGGREST_1.40.0 pillar_1.9.0
[55] fgsea_1.26.0 boot_1.3-28.1 codetools_0.2-19
[58] fastmatch_1.1-3 pan_1.8 glue_1.6.2
[61] ggfun_0.1.1 downloader_0.4 remotes_2.4.2
[64] vcd_1.4-11 treeio_1.24.1 vctrs_0.6.3
[67] png_0.1-8 gtable_0.3.3 cachem_1.0.8
[70] mime_0.12 tidygraph_1.2.3 pcaPP_2.0-3
[73] survival_3.5-5 iterators_1.0.14 ellipsis_0.3.2
[76] nlme_3.1-162 ggtree_3.8.0 bit64_4.0.5
[79] GenomeInfoDb_1.36.1 rprojroot_2.0.3 bslib_0.5.0
[82] rpart_4.1.19 DBI_1.1.3 nnet_7.3-19
[85] tidyselect_1.2.0 processx_3.8.1 bit_4.0.5
[88] compiler_4.3.1 curl_5.0.1 desc_1.4.2
[91] shadowtext_0.1.2 scales_1.2.1 DEoptimR_1.0-14
[94] lmtest_0.9-40 callr_3.7.3 digest_0.6.32
[97] minqa_1.2.5 XVector_0.40.0 htmltools_0.5.5
[100] pkgconfig_2.0.3 lme4_1.1-33 fastmap_1.1.1
[103] rlang_1.1.1 htmlwidgets_1.6.2 farver_2.1.1
[106] jquerylib_0.1.4 zoo_1.8-12 jsonlite_1.8.5
[109] BiocParallel_1.34.2 GOSemSim_2.26.0 R.oo_1.25.0
[112] RCurl_1.98-1.12 ggplotify_0.1.1 GenomeInfoDbData_1.2.10 [115] patchwork_1.1.2 munsell_0.5.0 ape_5.7-1
[118] viridis_0.6.3 stringi_1.7.12 ggraph_2.1.0
[121] zlibbioc_1.46.0 MASS_7.3-60 plyr_1.8.8
[124] pkgbuild_1.4.2 ggrepel_0.9.3 parallel_4.3.1
[127] graphlayouts_1.0.0 Biostrings_2.68.1 splines_4.3.1
[130] hms_1.1.3 locfit_1.5-9.8 ps_1.7.5
[133] igraph_1.5.0 ranger_0.15.1 rngtools_1.5.2
[136] pkgload_1.3.2 BiocManager_1.30.21 laeken_0.5.2
[139] nloptr_2.0.3 tzdb_0.4.0 foreach_1.5.2
[142] tweenr_2.0.2 httpuv_1.6.11 polyclip_1.10-4
[145] ggforce_0.4.1 broom_1.0.5 xtable_1.8-4
[148] tidytree_0.4.2 later_1.3.1 viridisLite_0.4.2
[151] class_7.3-22 aplot_0.1.10 memoise_2.0.1
[154] cluster_2.1.4 timechange_0.2.0