select with org.Mm.eg.db does not give ENSEMBL ids
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raf4 ▴ 20
@raf4-8249
Last seen 7 days ago
United States

Dear org.Mm.eg.db Maintainer,

I canot get ENSEMBL IDS from org.Mm.eg.db. The analogous code works with org.Hs.eg.db Please advise or fix. I tried writing maintainer@bioconductor.org, but my e-mail was returned.

> library(org.Mm.eg.db) 
> 
> genessym<-read.table("data/genes_sym.txt",sep="\t",header=T,as.is=T)
> dim(genessym)
[1] 47  1
> ids<-genessym$SYMBOL
> ids
 [1] "Cacna1c" "Cacn1d"  "Cacna1s" "Cacna1g" "Cacna1h" "Cacna1i" "Cacnb1"  "Cacnb2"  "Cacnb3"  "Cacnb4"  "Rrad"    "Rem1"  
[13] "Rem2"    "Ryr1"    "Ryr2"    "Ryr3"    "Atp2a1"  "Atp2a2"  "Atp2a3"  "Adra1a"  "Adra2a"  "Adrb2"   "Adrb1"   "Myh11"  
[25] "Acta2"   "Agtr2"   "Itpr1"   "Itpr2"   "Itpr3"   "Prkca"   "Prkaca"  "Prkg1"   "Prkg2"   "Prkaa1"  "Prkaa2"  "Prkag1"
[37] "Prkar1a" "Prkar2a" "Prkab2"  "Prkacb"  "Ppp1ca"  "Ppp2ca"  "Ppp2ccb" "Sphk1"   "Sphk2"   "Rock1"   "Rock2"  
> select(org.Mm.eg.db, keys=ids, columns=c("SYMBOL","ENSEMBL"), keytype="SYMBOL") 
Error: unexpected input in "select(org.Mm.eg.db, keys=ids, columns=c("SYMBOL","ENSEMBL"), keytype="SYMBOL") "
> 
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.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] stats4    stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] org.Mm.eg.db_3.16.0  AnnotationDbi_1.60.0 IRanges_2.32.0       S4Vectors_0.36.1     Biobase_2.58.0       BiocGenerics_0.44.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9             XVector_0.38.0         zlibbioc_1.44.0        bit_4.0.5              R6_2.5.1              
 [6] rlang_1.0.6            fastmap_1.1.0          blob_1.2.3             httr_1.4.4             GenomeInfoDb_1.34.6  
[11] tools_4.2.2            png_0.1-8              cli_3.6.0              DBI_1.1.3              bit64_4.0.5          
[16] crayon_1.5.2           GenomeInfoDbData_1.2.9 bitops_1.0-7           vctrs_0.5.1            KEGGREST_1.38.0      
[21] RCurl_1.98-1.9         memoise_2.0.1          cachem_1.0.6           RSQLite_2.2.20         compiler_4.2.2        
[26] Biostrings_2.66.0      pkgconfig_2.0.3      
>

Thank you,

Richard Friedman

Columbia University Cancer Center

Biomedical Informatics Shared Resource

org.Mm.eg.db • 100 views
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Entering edit mode
Guido Hooiveld ★ 3.5k
@guido-hooiveld-2020
Last seen 8 hours ago
Wageningen University, Wageningen, the …

FWIW: your code is working in my hands; see below.

Two thoughts: confirm that your input is a character vector, and in case the function select is masked by another package you may want to explicitly specify to use the function from the library AnnotationDbi:

> AnnotationDbi::select(org.Mm.eg.db, keys=ids, columns=c("SYMBOL","ENSEMBL"), keytype="SYMBOL") 



> library(org.Mm.eg.db)
> ids <- c("Cacna1c","Cacn1d","Cacna1s","Cacna1g","Cacna1h","Cacna1i","Cacnb1","Cacnb2","Cacnb3","Cacnb4","Rrad","Rem1")
> select(org.Mm.eg.db, keys=ids, columns=c("SYMBOL","ENSEMBL"), keytype="SYMBOL") 
'select()' returned 1:1 mapping between keys and columns
    SYMBOL            ENSEMBL
1  Cacna1c ENSMUSG00000051331
2   Cacn1d               <NA>
3  Cacna1s ENSMUSG00000026407
4  Cacna1g ENSMUSG00000020866
5  Cacna1h ENSMUSG00000024112
6  Cacna1i ENSMUSG00000022416
7   Cacnb1 ENSMUSG00000020882
8   Cacnb2 ENSMUSG00000057914
9   Cacnb3 ENSMUSG00000003352
10  Cacnb4 ENSMUSG00000017412
11    Rrad ENSMUSG00000031880
12    Rem1 ENSMUSG00000000359
> class(ids)
[1] "character"
> sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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    

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

other attached packages:
[1] org.Mm.eg.db_3.16.0  AnnotationDbi_1.60.0 IRanges_2.32.0      
[4] S4Vectors_0.36.1     Biobase_2.58.0       BiocGenerics_0.44.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9             XVector_0.38.0         zlibbioc_1.44.0       
 [4] bit_4.0.5              R6_2.5.1               rlang_1.0.6           
 [7] fastmap_1.1.0          blob_1.2.3             httr_1.4.4            
[10] GenomeInfoDb_1.34.6    tools_4.2.2            png_0.1-8             
[13] cli_3.6.0              DBI_1.1.3              bit64_4.0.5           
[16] crayon_1.5.2           GenomeInfoDbData_1.2.9 bitops_1.0-7          
[19] vctrs_0.5.1            KEGGREST_1.38.0        RCurl_1.98-1.9        
[22] memoise_2.0.1          cachem_1.0.6           RSQLite_2.2.20        
[25] compiler_4.2.2         Biostrings_2.66.0      pkgconfig_2.0.3       
> 
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Entering edit mode

Guido,

Thank you very much. It turned out that I had an extra invisible character in my select command which I had pasted in. When I removed it, the comand worked with just select.

Best wishes,

Rich

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