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I used the data in org.Hs.eg.db and AnnotationForge to build a local OrgDb, but when I used this OrgDb to run enrichGO, I got the following error. Can anyone tell me how to resolve?
rlibrary(RSQLite)
library(org.Hs.eg.db)
library(dplyr)
library(stringr)
library(AnnotationForge)
library(tidyverse)
options(stringsAsFactors = F)
result <- select(org.Hs.eg.db,
keys = keys(org.Hs.eg.db, keytype = "ENTREZID"),
columns = c("ENSEMBL", "GENENAME", "SYMBOL", "UNIPROT", "GO"),
keytype = "ENTREZID")
data <- result %>% dplyr::select(GID=ENTREZID, Gene_Name=GENENAME, Gene_Symbol=SYMBOL,
Gene_Ensembl=ENSEMBL, Gene_Uniprot=UNIPROT, GO=GO,
EVIDENCE=EVIDENCE)
gene_info <- dplyr::select(data,GID,Gene_Name) %>%
dplyr::filter(!is.na(Gene_Name))
gene2symbol <- dplyr::select(data,GID,Gene_Symbol) %>%
dplyr::filter(!is.na(Gene_Symbol))
gene2ensembl <- dplyr::select(data,GID,Gene_Ensembl) %>%
dplyr::filter(!is.na(Gene_Ensembl))
gene2uniprot <- dplyr::select(data,GID,Gene_Uniprot) %>%
dplyr::filter(!is.na(Gene_Uniprot))
gene2go <- dplyr::select(data,GID,GO,EVIDENCE) %>%
dplyr::filter(GO!=" ",!is.na(GO))
# remove duplication
gene_info <- unique(gene_info)
gene2symbol <- unique(gene2symbol)
gene2ensembl <- unique(gene2ensembl)
gene2uniprot <- unique(gene2uniprot)
gene2go <- unique(gene2go)
# build
AnnotationForge::makeOrgPackage(gene_info=gene_info,
go=gene2go,
symbol=gene2symbol,
ensembl=gene2ensembl,
uniprot=gene2uniprot,
maintainer='xxx<xxx@fxxx.com>',
author='xxx',
version="1.0" ,
outputDir=getwd(),
tax_id="9606",
genus="Homo",
species="sapiens",
goTable="go")
# Terminal run：R CMD build org.Hsapiens.eg.db
install.packages('org.Hsapiens.eg.db_1.0.tar.gz', repos = NULL)
library(org.Hsapiens.eg.db)
library(clusterProfiler)
symbolList <- c("GPX3", "GLRX", "LBP", "CRYAB", "DEFB1")
eg <- bitr(symbolList,
fromType="SYMBOL",
toType=c("GID","ENSEMBL","UNIPROT"),
OrgDb="org.Hsapiens.eg.db")
genelist <- eg$UNIPROT
genelist = genelist[!duplicated(genelist)]
go <- enrichGO(genelist,
OrgDb = org.Hsapiens.eg.db,
ont='ALL',
pAdjustMethod = 'BH',
pvalueCutoff = 1,
qvalueCutoff = 1,
keyType = 'UNIPROT',
readable = T)
head(go)
**# ERROR**
> go <- enrichGO(genelist,
+ OrgDb = org.Hsapiens.eg.db,
+ ont='ALL',
+ pAdjustMethod = 'BH',
+ pvalueCutoff = 1,
+ qvalueCutoff = 1,
+ keyType = 'UNIPROT',
+ readable = T)
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'GOALL'. Please use the keys method to see a listing of valid arguments.
sessionInfo( )
> sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8
[4] LC_COLLATE=zh_CN.UTF-8 LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[3] OrganismDbi_1.36.0 GenomicFeatures_1.46.5
[5] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[7] RSQLite_2.3.0 org.Mmusculus.eg.db_1.0
[9] org.Mm.eg.db_3.14.0 clusterProfiler_4.2.2
[11] org.Hsapiens.eg.db_1.0 lubridate_1.9.2
[13] forcats_1.0.0 purrr_1.0.1
[15] tidyr_1.3.0 tibble_3.2.1
[17] ggplot2_3.4.2 tidyverse_2.0.0
[19] AnnotationForge_1.36.0 stringr_1.5.0
[21] dplyr_1.1.2 devtools_2.4.5
[23] usethis_2.1.6 ComplexHeatmap_2.10.0
[25] ggstatsplot_0.11.1 limma_3.50.3
[27] future.apply_1.10.0 future_1.32.0
[29] readxl_1.4.2 topGO_2.46.0
[31] SparseM_1.81 GO.db_3.14.0
[33] graph_1.72.0 DOSE_3.20.1
[35] org.Hs.eg.db_3.14.0 AnnotationDbi_1.56.2
[37] IRanges_2.28.0 S4Vectors_0.32.4
[39] Biobase_2.54.0 BiocGenerics_0.40.0
[41] readr_2.1.4 RCurl_1.98-1.12
loaded via a namespace (and not attached):
[1] estimability_1.4.1 rappdirs_0.3.3 rtracklayer_1.54.0
[4] coda_0.19-4 bit64_4.0.5 DelayedArray_0.20.0
[7] data.table_1.14.8 KEGGREST_1.34.0 doParallel_1.0.17
[10] generics_0.1.3 callr_3.7.3 shadowtext_0.1.2
[13] correlation_0.8.4 bit_4.0.5 tzdb_0.3.0
[16] enrichplot_1.14.2 xml2_1.3.3 httpuv_1.6.9
[19] SummarizedExperiment_1.24.0 viridis_0.6.2 hms_1.1.3
[22] promises_1.2.0.1 fansi_1.0.4 restfulr_0.0.15
[25] progress_1.2.2 dbplyr_2.3.2 igraph_1.4.2
[28] DBI_1.1.3 htmlwidgets_1.6.2 paletteer_1.5.0
[31] ellipsis_0.3.2 insight_0.19.1 biomaRt_2.50.3
[34] MatrixGenerics_1.6.0 vctrs_0.6.1 remotes_2.4.2
[37] cachem_1.0.7 withr_2.5.0 ggforce_0.4.1
[40] vroom_1.6.1 emmeans_1.8.5 GenomicAlignments_1.30.0
[43] treeio_1.23.1 prettyunits_1.1.1 cluster_2.1.4
[46] ape_5.7-1 lazyeval_0.2.2 crayon_1.5.2
[49] pkgconfig_2.0.3 tweenr_2.0.2 nlme_3.1-162
[52] statsExpressions_1.5.0 pkgload_1.3.2 rlang_1.1.0
[55] globals_0.16.2 lifecycle_1.0.3 miniUI_0.1.1.1
[58] downloader_0.4 filelock_1.0.2 BiocFileCache_2.2.1
[61] cellranger_1.1.0 polyclip_1.10-4 matrixStats_0.63.0
[64] datawizard_0.7.1 Matrix_1.5-4 aplot_0.1.10
[67] GlobalOptions_0.1.2 processx_3.8.1 png_0.1-8
[70] viridisLite_0.4.1 rjson_0.2.21 parameters_0.21.0
[73] bitops_1.0-7 Biostrings_2.62.0 blob_1.2.4
[76] shape_1.4.6 qvalue_2.26.0 parallelly_1.35.0
[79] gridGraphics_0.5-1 scales_1.2.1 memoise_2.0.1
[82] magrittr_2.0.3 plyr_1.8.8 zlibbioc_1.40.0
[85] compiler_4.1.2 scatterpie_0.1.8 BiocIO_1.4.0
[88] RColorBrewer_1.1-3 clue_0.3-64 Rsamtools_2.10.0
[91] cli_3.6.1 XVector_0.34.0 urlchecker_1.0.1
[94] listenv_0.9.0 patchwork_1.1.2 ps_1.7.5
[97] MASS_7.3-58.3 tidyselect_1.2.0 stringi_1.7.12
[100] yaml_2.3.7 GOSemSim_2.20.0 ggrepel_0.9.3
[103] fastmatch_1.1-3 tools_4.1.2 timechange_0.2.0
[106] parallel_4.1.2 circlize_0.4.15 rstudioapi_0.14
[109] foreach_1.5.2 gridExtra_2.3 farver_2.1.1
[112] ggraph_2.1.0 digest_0.6.31 BiocManager_1.30.20
[115] shiny_1.7.4 Rcpp_1.0.10 later_1.3.0
[118] httr_1.4.5 colorspace_2.1-0 XML_3.99-0.14
[121] fs_1.6.1 splines_4.1.2 yulab.utils_0.0.6
[124] RBGL_1.70.0 rematch2_2.1.2 tidytree_0.4.2
[127] graphlayouts_0.8.4 ggplotify_0.1.0 sessioninfo_1.2.2
[130] xtable_1.8-4 jsonlite_1.8.4 ggtree_3.7.2
[133] tidygraph_1.2.3 zeallot_0.1.0 ggfun_0.0.9
[136] R6_2.5.1 profvis_0.3.7 pillar_1.9.0
[139] htmltools_0.5.5 mime_0.12 glue_1.6.2
[142] fastmap_1.1.1 BiocParallel_1.28.3 codetools_0.2-19
[145] fgsea_1.20.0 pkgbuild_1.4.0 mvtnorm_1.1-3
[148] utf8_1.2.3 lattice_0.21-8 curl_5.0.0
[151] munsell_0.5.0 DO.db_2.9 GetoptLong_1.0.5
[154] GenomeInfoDbData_1.2.7 iterators_1.0.14 reshape2_1.4.4
[157] gtable_0.3.3 bayestestR_0.13.1
