Problem select / ensembl package
2
0
Entering edit mode
yinnahm • 0
@5459c359
Last seen 14 days ago
Mexico

I want to get the annotation for a list of genes whose identifier is ensembl, but when I try to use select it give an error. Then I used the example from the documentation to get some annotations and the error was the same. I do not understand what is wrong

BiocManager::install("EnsDb.Hsapiens.v86", force=TRUE)
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
library(dplyr)
select(edb, keys = c("BCL2", "BCL2L11"), keytype = "GENENAME",
       columns = c("GENEID", "GENENAME", "TXID", "TXBIOTYPE"))

##ERROR

Error in UseMethod("select") : 
  no applicable method for 'select' applied to an object of class "EnsDb" 

sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

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

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

other attached packages:
 [1] dplyr_1.0.7               EnsDb.Hsapiens.v86_2.99.0
 [3] ensembldb_2.16.4          AnnotationFilter_1.16.0  
 [5] GenomicFeatures_1.44.2    AnnotationDbi_1.54.1     
 [7] Biobase_2.52.0            GenomicRanges_1.44.0     
 [9] GenomeInfoDb_1.28.4       IRanges_2.26.0           
[11] S4Vectors_0.30.2          BiocGenerics_0.38.0      

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.4.3        httr_1.4.2                 
 [3] bit64_4.0.5                 assertthat_0.2.1           
 [5] BiocManager_1.30.16         BiocFileCache_2.0.0        
 [7] blob_1.2.2                  GenomeInfoDbData_1.2.6     
 [9] Rsamtools_2.8.0             yaml_2.2.1                 
[11] progress_1.2.2              pillar_1.6.4               
[13] RSQLite_2.2.8               lattice_0.20-45            
[15] glue_1.4.2                  digest_0.6.28              
[17] XVector_0.32.0              Matrix_1.3-4               
[19] XML_3.99-0.8                pkgconfig_2.0.3            
[21] biomaRt_2.48.3              zlibbioc_1.38.0            
[23] purrr_0.3.4                 BiocParallel_1.26.2        
[25] tibble_3.1.5                KEGGREST_1.32.0            
[27] generics_0.1.1              ellipsis_0.3.2             
[29] cachem_1.0.6                SummarizedExperiment_1.22.0
[31] lazyeval_0.2.2              magrittr_2.0.1             
[33] crayon_1.4.1                memoise_2.0.0              
[35] fansi_0.5.0                 xml2_1.3.2                 
[37] tools_4.1.1                 prettyunits_1.1.1          
[39] hms_1.1.1                   BiocIO_1.2.0               
[41] lifecycle_1.0.1             matrixStats_0.61.0         
[43] stringr_1.4.0               DelayedArray_0.18.0        
[45] Biostrings_2.60.2           compiler_4.1.1             
[47] rlang_0.4.12                grid_4.1.1                 
[49] RCurl_1.98-1.5              rstudioapi_0.13            
[51] rjson_0.2.20                rappdirs_0.3.3             
[53] bitops_1.0-7                restfulr_0.0.13            
[55] DBI_1.1.1                   curl_4.3.2                 
[57] R6_2.5.1                    GenomicAlignments_1.28.0   
[59] rtracklayer_1.52.1          fastmap_1.1.0              
[61] bit_4.0.4                   utf8_1.2.2                 
[63] filelock_1.0.2              ProtGenerics_1.24.0        
[65] stringi_1.7.5               Rcpp_1.0.7                 
[67] vctrs_0.3.8                 png_0.1-7                  
[69] dbplyr_2.1.1                tidyselect_1.1.1
ensembldb • 138 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 7 days ago
United States

Looks like select is being masked by the tidyverse. Try using the fully qualified name ensembldb::select

0
Entering edit mode

For example

> select(EnsDb.Hsapiens.v75, head(keys(EnsDb.Hsapiens.v75)), "SYMBOL")
Error in UseMethod("select") : 
  no applicable method for 'select' applied to an object of class "EnsDb"
> ensembldb::select(EnsDb.Hsapiens.v75, head(keys(EnsDb.Hsapiens.v75)), "SYMBOL")
           GENEID   SYMBOL
1 ENSG00000000003   TSPAN6
2 ENSG00000000005     TNMD
3 ENSG00000000419     DPM1
4 ENSG00000000457    SCYL3
5 ENSG00000000460 C1orf112
6 ENSG00000000938      FGR
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0
Entering edit mode
yinnahm • 0
@5459c359
Last seen 14 days ago
Mexico

ensembldb::select works perfect

Thanks!!!

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