mapping mouse ENSEMBL ids to human gene symbol
1
0
Entering edit mode
cosomol999 • 0
@7fc3330e
Last seen 15 days ago
USA

I am trying to map mouse ENSEMBL ids to human gene symbols. However I am getting error

Error in names(destIDs) <- dnames : attempt to set an attribute on NULL

Here is my code:


library(org.Hs.eg.db)
library(org.Mm.eg.db)
library(hom.Hs.inp.db)
library(hom.Mm.inp.db)

v <- c('ENSMUSG00000059552', 'ENSMUSG00000020122') # ids for P53 and EGFR

inpIDMapper(v, "MUSMU", "HOMSA", srcIDType="ENSEMBL")
# Error in names(destIDs) <- dnames : attempt to set an attribute on NULL

sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 20.2

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_CA.UTF-8      
 [2] LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8       
 [4] LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8   
 [6] LC_MESSAGES=en_CA.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8      
 [8] LC_NAME=C                 
 [9] LC_ADDRESS=C              
[10] LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8
[12] LC_IDENTIFICATION=C       

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

other attached packages:
[1] hom.Mm.inp.db_3.1.3  hom.Hs.inp.db_3.1.3 
[3] org.Mm.eg.db_3.12.0  org.Hs.eg.db_3.11.4 
[5] AnnotationDbi_1.52.0 IRanges_2.22.2      
[7] S4Vectors_0.26.1     Biobase_2.48.0      
[9] BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7          DBI_1.1.1          
 [3] RSQLite_2.2.7       cachem_1.0.5       
 [5] rlang_0.4.11        blob_1.2.1         
 [7] vctrs_0.3.8         tools_4.0.3        
 [9] bit64_4.0.5         bit_4.0.4          
[11] fastmap_1.1.0       compiler_4.0.3     
[13] pkgconfig_2.0.3     BiocManager_1.30.16
[15] memoise_2.0.0
Annotation AnnotationDbi annotate • 104 views
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1
Entering edit mode
@kevin
Last seen 10 hours ago
Republic of Ireland

Hey cosomol999,

You could try biomaRt, if you wished (you can try biomaRt, if you wish):

require(biomaRt)
listDatasets(useMart('ensembl'))

human <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl')
mouse <- useMart('ensembl', dataset = 'mmusculus_gene_ensembl')

getLDS(
  mart = mouse,
  attributes = c('mgi_symbol','ensembl_gene_id','gene_biotype'),
  martL = human,
  attributesL = c('hgnc_symbol','ensembl_gene_id','gene_biotype'),
  filters = 'ensembl_gene_id',
  values = c('ENSMUSG00000059552', 'ENSMUSG00000020122'))

  MGI.symbol     Gene.stable.ID      Gene.type HGNC.symbol Gene.stable.ID.1
1      Trp53 ENSMUSG00000059552 protein_coding        TP53  ENSG00000141510
2       Egfr ENSMUSG00000020122 protein_coding        EGFR  ENSG00000146648
     Gene.type.1
1 protein_coding
2 protein_coding

Somebody else may have a solution via the packages that you had originally selected.

Kevin

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0
Entering edit mode

There's not to my knowledge a different solution if you are using Ensembl IDs (that doesn't involve mapping between NCBI and EBI IDs). The pure NCBI mapping is now handled by the Orthology.eg.db package, which replaces the old inParanoid based packages that the OP was trying to use.

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