Can't select GO from AnnotationHub orgDB packages
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Entering edit mode
Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 9 weeks ago
United States

Hello,

I am having a problem trying to pull GO (or EVIDENCE but not ONTOLOGY) terms from an OrgDB package from AnnotationHub; it's getting confused on the GO and GOALL keytypes:

> BiocManager::version()
[1] ‘3.11’
> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2020-04-27
> query(ah, c("OrgDb", "Daphnia"))
AnnotationHub with 1 record
...
# retrieve record with 'object[["AH81226"]]' 
> org.Dm.eg.db <- ah[["AH81226"]]

> temp <- select(org.Dm.eg.db, keys = keys(org.Dm.eg.db, keytype = "ENTREZID"),
+                keytype = "ENTREZID", columns = c("GO"))
Error in FUN(X[[i]], ...) : 
  Two fields in the source DB have the same name.

> keytypes(org.Dm.eg.db)
 [1] "ACCNUM"      "ALIAS"       "ENTREZID"    "EVIDENCE"   
 [5] "EVIDENCEALL" "GENENAME"    "GID"         "GO"         
 [9] "GOALL"       "ONTOLOGY"    "ONTOLOGYALL" "PMID"       
[13] "REFSEQ"      "SYMBOL"

#check the others:
> temp <- select(org.Dm.eg.db, keys = keys(org.Dm.eg.db, keytype = "ENTREZID"),
+                keytype = "ENTREZID", columns = c("EVIDENCE"))
Error in FUN(X[[i]], ...) : 
  Two fields in the source DB have the same name.
> temp <- select(org.Dm.eg.db, keys = keys(org.Dm.eg.db, keytype = "ENTREZID"),
+                keytype = "ENTREZID", columns = c("ONTOLOGY"))
'select()' returned 1:many mapping between keys and columns

Didn't this same error happen in the pre-built OrgDB right when 3.11 was released? That appears to be fixed:

> library(org.Mm.eg.db)

> temp <- select(org.Mm.eg.db, keys = keys(org.Mm.eg.db, keytype = "ENTREZID"),
+                keytype = "ENTREZID", columns = c("GO"))
'select()' returned 1:many mapping between keys and columns

Thanks!

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] org.Mm.eg.db_3.11.4  AnnotationDbi_1.50.1 IRanges_2.22.2      
[4] S4Vectors_0.26.1     Biobase_2.48.0       AnnotationHub_2.20.0
[7] BiocFileCache_1.12.0 dbplyr_1.4.4         BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5                    later_1.1.0.1                
 [3] pillar_1.4.6                  compiler_4.0.2               
 [5] BiocManager_1.30.10           tools_4.0.2                  
 [7] digest_0.6.25                 bit_1.1-15.2                 
 [9] RSQLite_2.2.0                 memoise_1.1.0                
[11] lifecycle_0.2.0               tibble_3.0.3                 
[13] pkgconfig_2.0.3               rlang_0.4.7                  
[15] shiny_1.5.0                   DBI_1.1.0                    
[17] rstudioapi_0.11               curl_4.3                     
[19] yaml_2.2.1                    xfun_0.15                    
[21] fastmap_1.0.1                 dplyr_1.0.0                  
[23] httr_1.4.2                    generics_0.0.2               
[25] vctrs_0.3.2                   rappdirs_0.3.1               
[27] bit64_0.9-7.1                 tidyselect_1.1.0             
[29] glue_1.4.1                    R6_2.4.1                     
[31] purrr_0.3.4                   blob_1.2.1                   
[33] magrittr_1.5                  promises_1.1.1               
[35] htmltools_0.5.0               ellipsis_0.3.1               
[37] assertthat_0.2.1              xtable_1.8-4                 
[39] mime_0.9                      interactiveDisplayBase_1.26.3
[41] httpuv_1.5.4                  tinytex_0.24                 
[43] crayon_1.3.4                  BiocVersion_3.11.1 
GO.db AnnotationHub OrgDB • 196 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 4 hours ago
United States

Hi Jenny,

See here. You should be able to fix that by doing

library(BiocManager)
install("jmacdon/AnnotationDbi")

I sent a PR to Kayla for the same fix yesterday, so I am assuming it will appear via the regular channels in time.

ADD COMMENT
0
Entering edit mode

Thanks, Jim! It did fix it. (Unfortunately for me, Daphnia magna only has GO terms for 61 genes). Looking forward to seeing you virtually next week at BioC2020...

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