Having error with clusterProfiler::bitr
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Andrea • 0
@Andrea-24639
Last seen 7 months ago

Hi everyone, I'm having trouble with the bitr function which translates gene identifiers from one system to another. I post directly the line of code I want to use and I expose the question.

SYMBOLS <- c('GOLGA3','ABCA8','ACIN1')

Change <- clusterProfiler:: bitr(SYMBOLS,

                                           fromType = 'SYMBOL',

                                           toType = c('ENTREZID','ENSEMBL'),

                                           OrgDb = org.Hs.eg.db,

                                           drop = TRUE)

# Error Message

#Error in .testForValidKeys(x, keys, keytype, fks) : 
# None of the keys entered are valid keys for 'SYMBOL'. Please use the keys method to see a listing of valid arguments.

Given that I am working in Human the org.Hs.eg.db should be correct. What I'm failing with?

Thank you in advance

clusterProfiler • 179 views
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Entering edit mode
Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …

Your code is working in my hands:

> library(clusterProfiler)
> library(org.Hs.eg.db)
> 
> SYMBOLS <- c('GOLGA3','ABCA8','ACIN1')
> 
> Change <- clusterProfiler:: bitr(SYMBOLS,
+ fromType = 'SYMBOL',
+ toType = c('ENTREZID','ENSEMBL'),
+ OrgDb = org.Hs.eg.db,
+ drop = TRUE)
'select()' returned 1:1 mapping between keys and columns
> 
> Change
  SYMBOL ENTREZID         ENSEMBL
1 GOLGA3     2802 ENSG00000090615
2  ABCA8    10351 ENSG00000141338
3  ACIN1    22985 ENSG00000100813
> 
> sessionInfo()
R version 4.0.3 Patched (2020-12-21 r79668)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

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

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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] org.Hs.eg.db_3.12.0    AnnotationDbi_1.52.0   IRanges_2.24.1        
[4] S4Vectors_0.28.1       Biobase_2.50.0         BiocGenerics_0.36.0   
[7] clusterProfiler_3.18.0

loaded via a namespace (and not attached):
 [1] ggrepel_0.9.1       Rcpp_1.0.6          lattice_0.20-41    
 [4] GO.db_3.12.1        tidyr_1.1.2         assertthat_0.2.1   
 [7] digest_0.6.27       ggforce_0.3.2       R6_2.5.0           
[10] plyr_1.8.6          RSQLite_2.2.2       ggplot2_3.3.3      
[13] pillar_1.4.7        rlang_0.4.10        data.table_1.13.6  
[16] blob_1.2.1          Matrix_1.3-2        qvalue_2.22.0      
[19] splines_4.0.3       BiocParallel_1.24.1 downloader_0.4     
[22] stringr_1.4.0       igraph_1.2.6        polyclip_1.10-0    
[25] bit_4.0.4           munsell_0.5.0       scatterpie_0.1.5   
[28] fgsea_1.16.0        compiler_4.0.3      pkgconfig_2.0.3    
[31] tidyselect_1.1.0    tibble_3.0.5        gridExtra_2.3      
[34] graphlayouts_0.7.1  enrichplot_1.10.1   viridisLite_0.3.0  
[37] crayon_1.3.4        dplyr_1.0.3         MASS_7.3-53        
[40] grid_4.0.3          gtable_0.3.0        lifecycle_0.2.0    
[43] DBI_1.1.1           magrittr_2.0.1      scales_1.1.1       
[46] stringi_1.5.3       GOSemSim_2.16.1     farver_2.0.3       
[49] reshape2_1.4.4      viridis_0.5.1       DO.db_2.9          
[52] rvcheck_0.1.8       ellipsis_0.3.1      generics_0.1.0     
[55] vctrs_0.3.6         cowplot_1.1.1       fastmatch_1.1-0    
[58] RColorBrewer_1.1-2  tools_4.0.3         bit64_4.0.5        
[61] glue_1.4.2          tweenr_1.0.1        purrr_0.3.4        
[64] shadowtext_0.0.7    ggraph_2.0.4        colorspace_2.0-0   
[67] BiocManager_1.30.10 tidygraph_1.2.0     DOSE_3.16.0        
[70] memoise_1.1.0      
> 
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