OrgDb making for Sus scrofa(Ensembl geneID)
library(org.Sscrofa.eg.db)
keytypes(org.Sscrofa.eg.db)
# [1] "chromosome_name" "description"
# [3] "end_position" "ENSEMBL"
# [5] "ensembl_exon_id" "ensembl_gene_id_version"
# [7] "ensembl_transcript_id" "entrezgene_id"
# [9] "EVIDENCE" "EVIDENCEALL"
#[11] "external_gene_name" "gene_biotype"
#[13] "GID" "GO"
#[15] "GOALL" "ONTOLOGY"
#[17] "ONTOLOGYALL" "start_position"
#[19] "strand" "SYMBOL"
#[21] "transcript_biotype" "transcript_count"
#[23] "transcript_end" "transcript_start"
#[25] "transcription_start_site"Usage:
GO <- enrichGO(res$gene_id,
OrgDb = "org.Sscrofa.eg.db",
keyType = "ENSEMBL",
readable = T)SessionInfo:
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22631)
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
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.54.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.11 prettyunits_1.2.0 png_0.1-8
[4] ps_1.7.5 Biostrings_2.66.0 utf8_1.2.3
[7] digest_0.6.33 mime_0.12 BiocFileCache_2.9.1
[10] R6_2.5.1 GenomeInfoDb_1.34.9 stats4_4.2.3
[13] RSQLite_2.3.1 pillar_1.9.0 httr_1.4.7
[16] zlibbioc_1.44.0 rlang_1.1.1 progress_1.2.2
[19] curl_5.0.2 rstudioapi_0.15.0 miniUI_0.1.1.1
[22] callr_3.7.3 urlchecker_1.0.1 blob_1.2.4
[25] S4Vectors_0.36.2 devtools_2.4.5 stringr_1.5.0
[28] htmlwidgets_1.6.2 RCurl_1.98-1.12 bit_4.0.5
[31] shiny_1.7.5 compiler_4.2.3 httpuv_1.6.11
[34] pkgconfig_2.0.3 BiocGenerics_0.44.0 pkgbuild_1.4.2
[37] htmltools_0.5.6 tidyselect_1.2.0 KEGGREST_1.38.0
[40] tibble_3.2.1 GenomeInfoDbData_1.2.9 IRanges_2.32.0
[43] XML_3.99-0.14 fansi_1.0.4 withr_2.5.1
[46] crayon_1.5.2 dplyr_1.1.3 dbplyr_2.3.4
[49] later_1.3.1 rappdirs_0.3.3 bitops_1.0-7
[52] xtable_1.8-4 lifecycle_1.0.3 DBI_1.1.3
[55] magrittr_2.0.3 cli_3.6.1 stringi_1.7.12
[58] cachem_1.0.8 XVector_0.38.0 fs_1.6.3
[61] promises_1.2.1 remotes_2.4.2.1 xml2_1.3.5
[64] filelock_1.0.2 ellipsis_0.3.2 vctrs_0.6.3
[67] generics_0.1.3 tools_4.2.3 bit64_4.0.5
[70] Biobase_2.58.0 glue_1.6.2 purrr_1.0.2
[73] hms_1.1.3 processx_3.8.2 pkgload_1.3.3
[76] fastmap_1.1.1 AnnotationDbi_1.60.2 sessioninfo_1.2.2
[79] memoise_2.0.1 profvis_0.3.8 usethis_2.2.2