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Hi Zuguang, I am using the simplest script with simplifyEnrichment like:
go_sm <- go_sm$ID go_sm <- GO_similarity(go_sm) df = simplifyGO(go_sm, exclude_words = c("bacterium", "biotic"))
but the exclude_words parameter is not working. Any idea? thanks!
sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] parallel grid stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] simplifyEnrichment_1.6.1 decoupleR_2.2.2 kableExtra_1.3.4 [4] IlluminaHumanMethylationEPICmanifest_0.3.0 mgmtstp27_0.6-3 MASS_7.3-58.1 [7] methylumi_2.42.0 FDb.InfiniumMethylation.hg19_2.2.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [10] GenomicFeatures_1.48.4 reshape2_1.4.4 scales_1.2.1 [13] ade4_1.7-20 lumi_2.48.0 minfi_1.42.0 [16] bumphunter_1.38.0 locfit_1.5-9.6 iterators_1.0.14 [19] foreach_1.5.2 Biostrings_2.64.1 XVector_0.38.0 [22] readxl_1.4.1 DESeq2_1.36.0 sparrow_1.2.0 [25] clusterProfiler_4.4.4 EnhancedVolcano_1.14.0 cluster_2.1.4 [28] sva_3.44.0 BiocParallel_1.30.4 genefilter_1.78.0 [31] mgcv_1.8-41 nlme_3.1-160 ComplexHeatmap_2.12.1 [34] ggfortify_0.4.15 ggalt_0.4.0 ggrepel_0.9.2 [37] edgeR_3.38.4 vsn_3.66.0 limma_3.54.0 [40] dlookr_0.6.1 janitor_2.1.0 rms_6.3-0 [43] SparseM_1.81 Hmisc_4.7-2 Formula_1.2-4 [46] lattice_0.20-45 survminer_0.4.9 survival_3.4-0 [49] corrplot_0.92 ggdist_3.2.0 hrbrthemes_0.8.0 [52] viridis_0.6.2 viridisLite_0.4.1 ggpubr_0.5.0 [55] ggsignif_0.6.4 ggbump_0.1.99999 org.Hs.eg.db_3.15.0 [58] AnnotationDbi_1.58.0 aracne.networks_1.22.0 viper_1.30.0 [61] RColorBrewer_1.1-3 arsenal_3.6.3 forcats_0.5.2 [64] stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5 [67] readr_2.1.3 tidyr_1.2.1 tibble_3.1.8 [70] ggplot2_3.4.0 tidyverse_1.3.2 TCGAutils_1.16.1 [73] TCGAbiolinks_2.24.3 curatedTCGAData_1.18.0 MultiAssayExperiment_1.22.0 [76] SummarizedExperiment_1.28.0 Biobase_2.58.0 GenomicRanges_1.50.1 [79] GenomeInfoDb_1.34.3 IRanges_2.32.0 S4Vectors_0.36.0 [82] BiocGenerics_0.44.0 MatrixGenerics_1.10.0 matrixStats_0.63.0
loaded via a namespace (and not attached): [1] mixtools_1.2.0 graphlayouts_0.8.3 haven_2.5.1 vctrs_0.5.1 [5] beanplot_1.3.1 blob_1.2.3 later_1.3.0 DBI_1.1.3 [9] reactable_0.3.0 rappdirs_0.3.3 distributional_0.3.1 jpeg_0.1-9 [13] zlibbioc_1.44.0 MatrixModels_0.5-1 htmlwidgets_1.5.4 mvtnorm_1.1-3 [17] GlobalOptions_0.1.2 irlba_2.3.5.1 BiocSet_1.10.0 illuminaio_0.38.0 [21] tidygraph_1.2.2 Rcpp_1.0.9 KernSmooth_2.23-20 promises_1.2.0.1 [25] DelayedArray_0.24.0 RcppParallel_5.1.5 magick_2.7.3 graph_1.74.0 [29] fs_1.5.2 fastmatch_1.1-3 digest_0.6.30 png_0.1-7 [33] polspline_1.1.20 GenomicDataCommons_1.20.3 nor1mix_1.3-0 scatterpie_0.1.8 [37] DOSE_3.22.1 beepr_1.3 nleqslv_3.3.3 ggraph_2.1.0 [41] pkgconfig_2.0.3 GO.db_3.15.0 DelayedMatrixStats_1.18.2 circlize_0.4.15 [45] GetoptLong_1.0.5 xfun_0.35 zoo_1.8-11 tidyselect_1.2.0 [49] kernlab_0.9-31 rtracklayer_1.56.1 rlang_1.0.6 glue_1.6.2 [53] gdtools_0.2.4 modelr_0.1.10 labeling_0.4.2 httpuv_1.6.6 [57] class_7.3-20 preprocessCore_1.60.0 Rttf2pt1_1.3.11 TH.data_1.1-1 [61] DO.db_2.9 annotate_1.74.0 webshot_0.5.4 jsonlite_1.8.3 [65] sysfonts_0.8.8 bit_4.0.5 mime_0.12 systemfonts_1.0.4 [69] gridExtra_2.3 Rsamtools_2.12.0 stringi_1.7.8 TCGAbiolinksGUI.data_1.16.0 [73] quadprog_1.5-8 yulab.utils_0.0.5 bitops_1.0-7 cli_3.4.1 [77] rhdf5filters_1.8.0 maps_3.4.1 RSQLite_2.2.18 partykit_1.2-16 [81] libcoin_1.0-9 data.table_1.14.6 timechange_0.1.1 rstudioapi_0.14 [85] GenomicAlignments_1.32.1 qvalue_2.28.0 gridGraphics_0.5-1 survMisc_0.5.6 [89] dbplyr_2.2.1 segmented_1.6-1 lifecycle_1.0.3 ExperimentHub_2.4.0 [93] munsell_0.5.0 cellranger_1.1.0 proxyC_0.3.3 codetools_0.2-18 [97] htmlTable_2.4.1 ontologyIndex_2.10 xtable_1.8-4 googlesheets4_1.0.1 [101] BiocManager_1.30.19 abind_1.4-5 farver_2.1.1 km.ci_0.5-6 [105] AnnotationHub_3.4.0 askpass_1.1 aplot_0.1.8 ggtree_3.4.4 [109] BiocIO_1.6.0 GEOquery_2.64.2 patchwork_1.1.2 extrafontdb_1.0 [113] Matrix_1.5-3 tidytree_0.4.1 ellipsis_0.3.2 prettyunits_1.1.1 [117] lubridate_1.9.0 googledrive_2.0.0 reprex_2.0.2 mclust_6.0.0 [121] igraph_1.3.5 multtest_2.52.0 fgsea_1.22.0 NLP_0.2-1 [125] slam_0.1-50 gargle_1.2.1 htmltools_0.5.3 BiocFileCache_2.4.0 [129] yaml_2.3.6 utf8_1.2.2 plotly_4.10.1 interactiveDisplayBase_1.34.0 [133] XML_3.99-0.12 e1071_1.7-12 foreign_0.8-83 withr_2.5.0 [137] bit64_4.0.5 rngtools_1.5.2 doRNG_1.8.2 affyio_1.68.0 [141] multcomp_1.4-20 GOSemSim_2.22.0 memoise_2.0.1 evaluate_0.18 [145] geneplotter_1.74.0 tzdb_0.3.0 extrafont_0.18 curl_4.3.3 [149] fansi_1.0.3 GSEABase_1.58.0 checkmate_2.1.0 cachem_1.0.6 [153] interp_1.1-3 deldir_1.0-6 babelgene_22.9 proj4_1.0-11 [157] rjson_0.2.21 rstatix_0.7.1 clue_0.3-63 tools_4.2.0 [161] sandwich_3.0-2 magrittr_2.0.3 RCurl_1.98-1.9 proxy_0.4-27 [165] car_3.1-1 ape_5.6-2 ggplotify_0.1.0 xml2_1.3.3 [169] httr_1.4.4 assertthat_0.2.1 rmarkdown_2.18 R6_2.5.1 [173] Rhdf5lib_1.18.2 nnet_7.3-18 progress_1.2.2 KEGGREST_1.36.3 [177] treeio_1.20.2 shape_1.4.6 inum_1.0-4 BiocVersion_3.15.2 [181] HDF5Array_1.24.2 rhdf5_2.40.0 splines_4.2.0 snakecase_0.11.0 [185] carData_3.0-5 ggfun_0.0.9 colorspace_2.0-3 generics_0.1.3 [189] base64enc_0.1-3 pillar_1.8.1 tweenr_2.0.2 affy_1.76.0 [193] audio_0.1-10 GenomeInfoDbData_1.2.9 plyr_1.8.8 gtable_0.3.1 [197] pagedown_0.19 rvest_1.0.3 restfulr_0.0.15 knitr_1.41 [201] latticeExtra_0.6-30 shadowtext_0.1.2 biomaRt_2.52.0 fastmap_1.1.0 [205] doParallel_1.0.17 tm_0.7-9 quantreg_5.94 broom_1.0.1 [209] openssl_2.0.4 filelock_1.0.2 backports_1.4.1 showtext_0.9-5 [213] base64_2.0.1 enrichplot_1.16.2 scrime_1.3.5 hms_1.1.2 [217] ggforce_0.4.1 showtextdb_3.0 shiny_1.7.3 KMsurv_0.1-5 [221] ash_1.0-15 polyclip_1.10-4 siggenes_1.70.0 lazyeval_0.2.2 [225] crayon_1.5.2 downloader_0.4 sparseMatrixStats_1.8.0 reshape_0.8.9 [229] svglite_2.1.0 rpart_4.1.19 compiler_4.2.0
The text was updated successfully, but these errors were encountered:
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Hi Zuguang,
I am using the simplest script with simplifyEnrichment like:
go_sm <- go_sm$ID
go_sm <- GO_similarity(go_sm)
df = simplifyGO(go_sm, exclude_words = c("bacterium", "biotic"))
but the exclude_words parameter is not working.
Any idea? thanks!
sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] simplifyEnrichment_1.6.1 decoupleR_2.2.2 kableExtra_1.3.4
[4] IlluminaHumanMethylationEPICmanifest_0.3.0 mgmtstp27_0.6-3 MASS_7.3-58.1
[7] methylumi_2.42.0 FDb.InfiniumMethylation.hg19_2.2.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[10] GenomicFeatures_1.48.4 reshape2_1.4.4 scales_1.2.1
[13] ade4_1.7-20 lumi_2.48.0 minfi_1.42.0
[16] bumphunter_1.38.0 locfit_1.5-9.6 iterators_1.0.14
[19] foreach_1.5.2 Biostrings_2.64.1 XVector_0.38.0
[22] readxl_1.4.1 DESeq2_1.36.0 sparrow_1.2.0
[25] clusterProfiler_4.4.4 EnhancedVolcano_1.14.0 cluster_2.1.4
[28] sva_3.44.0 BiocParallel_1.30.4 genefilter_1.78.0
[31] mgcv_1.8-41 nlme_3.1-160 ComplexHeatmap_2.12.1
[34] ggfortify_0.4.15 ggalt_0.4.0 ggrepel_0.9.2
[37] edgeR_3.38.4 vsn_3.66.0 limma_3.54.0
[40] dlookr_0.6.1 janitor_2.1.0 rms_6.3-0
[43] SparseM_1.81 Hmisc_4.7-2 Formula_1.2-4
[46] lattice_0.20-45 survminer_0.4.9 survival_3.4-0
[49] corrplot_0.92 ggdist_3.2.0 hrbrthemes_0.8.0
[52] viridis_0.6.2 viridisLite_0.4.1 ggpubr_0.5.0
[55] ggsignif_0.6.4 ggbump_0.1.99999 org.Hs.eg.db_3.15.0
[58] AnnotationDbi_1.58.0 aracne.networks_1.22.0 viper_1.30.0
[61] RColorBrewer_1.1-3 arsenal_3.6.3 forcats_0.5.2
[64] stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5
[67] readr_2.1.3 tidyr_1.2.1 tibble_3.1.8
[70] ggplot2_3.4.0 tidyverse_1.3.2 TCGAutils_1.16.1
[73] TCGAbiolinks_2.24.3 curatedTCGAData_1.18.0 MultiAssayExperiment_1.22.0
[76] SummarizedExperiment_1.28.0 Biobase_2.58.0 GenomicRanges_1.50.1
[79] GenomeInfoDb_1.34.3 IRanges_2.32.0 S4Vectors_0.36.0
[82] BiocGenerics_0.44.0 MatrixGenerics_1.10.0 matrixStats_0.63.0
loaded via a namespace (and not attached):
[1] mixtools_1.2.0 graphlayouts_0.8.3 haven_2.5.1 vctrs_0.5.1
[5] beanplot_1.3.1 blob_1.2.3 later_1.3.0 DBI_1.1.3
[9] reactable_0.3.0 rappdirs_0.3.3 distributional_0.3.1 jpeg_0.1-9
[13] zlibbioc_1.44.0 MatrixModels_0.5-1 htmlwidgets_1.5.4 mvtnorm_1.1-3
[17] GlobalOptions_0.1.2 irlba_2.3.5.1 BiocSet_1.10.0 illuminaio_0.38.0
[21] tidygraph_1.2.2 Rcpp_1.0.9 KernSmooth_2.23-20 promises_1.2.0.1
[25] DelayedArray_0.24.0 RcppParallel_5.1.5 magick_2.7.3 graph_1.74.0
[29] fs_1.5.2 fastmatch_1.1-3 digest_0.6.30 png_0.1-7
[33] polspline_1.1.20 GenomicDataCommons_1.20.3 nor1mix_1.3-0 scatterpie_0.1.8
[37] DOSE_3.22.1 beepr_1.3 nleqslv_3.3.3 ggraph_2.1.0
[41] pkgconfig_2.0.3 GO.db_3.15.0 DelayedMatrixStats_1.18.2 circlize_0.4.15
[45] GetoptLong_1.0.5 xfun_0.35 zoo_1.8-11 tidyselect_1.2.0
[49] kernlab_0.9-31 rtracklayer_1.56.1 rlang_1.0.6 glue_1.6.2
[53] gdtools_0.2.4 modelr_0.1.10 labeling_0.4.2 httpuv_1.6.6
[57] class_7.3-20 preprocessCore_1.60.0 Rttf2pt1_1.3.11 TH.data_1.1-1
[61] DO.db_2.9 annotate_1.74.0 webshot_0.5.4 jsonlite_1.8.3
[65] sysfonts_0.8.8 bit_4.0.5 mime_0.12 systemfonts_1.0.4
[69] gridExtra_2.3 Rsamtools_2.12.0 stringi_1.7.8 TCGAbiolinksGUI.data_1.16.0
[73] quadprog_1.5-8 yulab.utils_0.0.5 bitops_1.0-7 cli_3.4.1
[77] rhdf5filters_1.8.0 maps_3.4.1 RSQLite_2.2.18 partykit_1.2-16
[81] libcoin_1.0-9 data.table_1.14.6 timechange_0.1.1 rstudioapi_0.14
[85] GenomicAlignments_1.32.1 qvalue_2.28.0 gridGraphics_0.5-1 survMisc_0.5.6
[89] dbplyr_2.2.1 segmented_1.6-1 lifecycle_1.0.3 ExperimentHub_2.4.0
[93] munsell_0.5.0 cellranger_1.1.0 proxyC_0.3.3 codetools_0.2-18
[97] htmlTable_2.4.1 ontologyIndex_2.10 xtable_1.8-4 googlesheets4_1.0.1
[101] BiocManager_1.30.19 abind_1.4-5 farver_2.1.1 km.ci_0.5-6
[105] AnnotationHub_3.4.0 askpass_1.1 aplot_0.1.8 ggtree_3.4.4
[109] BiocIO_1.6.0 GEOquery_2.64.2 patchwork_1.1.2 extrafontdb_1.0
[113] Matrix_1.5-3 tidytree_0.4.1 ellipsis_0.3.2 prettyunits_1.1.1
[117] lubridate_1.9.0 googledrive_2.0.0 reprex_2.0.2 mclust_6.0.0
[121] igraph_1.3.5 multtest_2.52.0 fgsea_1.22.0 NLP_0.2-1
[125] slam_0.1-50 gargle_1.2.1 htmltools_0.5.3 BiocFileCache_2.4.0
[129] yaml_2.3.6 utf8_1.2.2 plotly_4.10.1 interactiveDisplayBase_1.34.0
[133] XML_3.99-0.12 e1071_1.7-12 foreign_0.8-83 withr_2.5.0
[137] bit64_4.0.5 rngtools_1.5.2 doRNG_1.8.2 affyio_1.68.0
[141] multcomp_1.4-20 GOSemSim_2.22.0 memoise_2.0.1 evaluate_0.18
[145] geneplotter_1.74.0 tzdb_0.3.0 extrafont_0.18 curl_4.3.3
[149] fansi_1.0.3 GSEABase_1.58.0 checkmate_2.1.0 cachem_1.0.6
[153] interp_1.1-3 deldir_1.0-6 babelgene_22.9 proj4_1.0-11
[157] rjson_0.2.21 rstatix_0.7.1 clue_0.3-63 tools_4.2.0
[161] sandwich_3.0-2 magrittr_2.0.3 RCurl_1.98-1.9 proxy_0.4-27
[165] car_3.1-1 ape_5.6-2 ggplotify_0.1.0 xml2_1.3.3
[169] httr_1.4.4 assertthat_0.2.1 rmarkdown_2.18 R6_2.5.1
[173] Rhdf5lib_1.18.2 nnet_7.3-18 progress_1.2.2 KEGGREST_1.36.3
[177] treeio_1.20.2 shape_1.4.6 inum_1.0-4 BiocVersion_3.15.2
[181] HDF5Array_1.24.2 rhdf5_2.40.0 splines_4.2.0 snakecase_0.11.0
[185] carData_3.0-5 ggfun_0.0.9 colorspace_2.0-3 generics_0.1.3
[189] base64enc_0.1-3 pillar_1.8.1 tweenr_2.0.2 affy_1.76.0
[193] audio_0.1-10 GenomeInfoDbData_1.2.9 plyr_1.8.8 gtable_0.3.1
[197] pagedown_0.19 rvest_1.0.3 restfulr_0.0.15 knitr_1.41
[201] latticeExtra_0.6-30 shadowtext_0.1.2 biomaRt_2.52.0 fastmap_1.1.0
[205] doParallel_1.0.17 tm_0.7-9 quantreg_5.94 broom_1.0.1
[209] openssl_2.0.4 filelock_1.0.2 backports_1.4.1 showtext_0.9-5
[213] base64_2.0.1 enrichplot_1.16.2 scrime_1.3.5 hms_1.1.2
[217] ggforce_0.4.1 showtextdb_3.0 shiny_1.7.3 KMsurv_0.1-5
[221] ash_1.0-15 polyclip_1.10-4 siggenes_1.70.0 lazyeval_0.2.2
[225] crayon_1.5.2 downloader_0.4 sparseMatrixStats_1.8.0 reshape_0.8.9
[229] svglite_2.1.0 rpart_4.1.19 compiler_4.2.0
The text was updated successfully, but these errors were encountered: