I'm using Biomart package after differential expression analysis with DESeq2 package. I used ENSEMBL ID. After differential analysis I would like to obtain the HGNC symbol or VGNC symbol from ENSEMBL ID. The following function work for HGNC symbol but I failed to retrieve vgnc gene name.

add.anns <- function(df, mart, ...)
{
  nm <- rownames(df)
  anns <- getBM(
    attributes = c("ensembl_gene_id", "hgnc_symbol","vgnc_genename", "description"),
    filters = "ensembl_gene_id", values = nm, mart = mart)
  anns <- anns[match(nm, anns[, 1]), ]
  colnames(anns) <- c("ID", "Gene Symbol", "Gene Description")
  df <- cbind(anns, df[, 2:ncol(df)])
  rownames(df) <- nm
  df
  }

Can you  tell me if there is an attribute to obtain vgnc gene name because I failed to obtained it (didn't find it with listAttributes(mart) ) .

Thank you in advance.

By the way your url retrieves  "404 not found error".

Regards

Carine

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages:
 [1] biomaRt_2.36.1              org.Bt.eg.db_3.6.0          AnnotationDbi_1.42.1       
 [4] ReportingTools_2.20.0       bindrcpp_0.2.2              DESeq2_1.20.0              
 [7] dplyr_0.7.6                 factoextra_1.0.5            ggplot2_3.0.0              
[10] ade4_1.7-11                 knitr_1.20                  SummarizedExperiment_1.10.1
[13] DelayedArray_0.6.2          BiocParallel_1.14.2         matrixStats_0.54.0         
[16] Biobase_2.40.0              GenomicRanges_1.32.6        GenomeInfoDb_1.16.0        
[19] IRanges_2.14.10             S4Vectors_0.18.3            BiocGenerics_0.26.0        

loaded via a namespace (and not attached):
  [1] backports_1.1.2          GOstats_2.46.0           Hmisc_4.1-1             
  [4] plyr_1.8.4               lazyeval_0.2.1           GSEABase_1.42.0         
  [7] splines_3.5.1            digest_0.6.15            BiocInstaller_1.30.0    
 [10] ensembldb_2.4.1          htmltools_0.3.6          GO.db_3.6.0             
 [13] magrittr_1.5             checkmate_1.8.5          memoise_1.1.0           
 [16] BSgenome_1.48.0          cluster_2.0.7-1          limma_3.36.2            
 [19] Biostrings_2.48.0        annotate_1.58.0          R.utils_2.6.0           
 [22] ggbio_1.28.4             prettyunits_1.0.2        colorspace_1.3-2        
 [25] apeglm_1.2.0             ggrepel_0.8.0            blob_1.1.1              
 [28] crayon_1.3.4             RCurl_1.95-4.11          graph_1.58.0            
 [31] genefilter_1.62.0        bindr_0.1.1              VariantAnnotation_1.26.1
 [34] survival_2.42-3          glue_1.3.0               gtable_0.2.0            
 [37] zlibbioc_1.26.0          XVector_0.20.0           Rgraphviz_2.24.0        
 [40] scales_0.5.0             GGally_1.4.0             DBI_1.0.0               
 [43] edgeR_3.22.3             Rcpp_0.12.18             emdbook_1.3.10          
 [46] htmlTable_1.12           xtable_1.8-2             progress_1.2.0          
 [49] foreign_0.8-70           bit_1.1-14               OrganismDbi_1.22.0      
 [52] Formula_1.2-3            AnnotationForge_1.22.1   httr_1.3.1              
 [55] htmlwidgets_1.2          RColorBrewer_1.1-2       acepack_1.4.1           
 [58] R.methodsS3_1.7.1        reshape_0.8.7            pkgconfig_2.0.1         
 [61] XML_3.98-1.12            nnet_7.3-12              locfit_1.5-9.1          
 [64] reshape2_1.4.3           tidyselect_0.2.4         rlang_0.2.1             
 [67] munsell_0.5.0            tools_3.5.1              RSQLite_2.1.1           
 [70] stringr_1.3.1            yaml_2.2.0               bit64_0.9-7             
 [73] purrr_0.2.5              AnnotationFilter_1.4.0   RBGL_1.56.0             
 [76] R.oo_1.22.0              compiler_3.5.1           rstudioapi_0.7          
 [79] curl_3.2                 PFAM.db_3.6.0            geneplotter_1.58.0      
 [82] tibble_1.4.2             stringi_1.1.7            GenomicFeatures_1.32.0  
 [85] lattice_0.20-35          ProtGenerics_1.12.0      Matrix_1.2-14           
 [88] pillar_1.3.0             data.table_1.11.4        bitops_1.0-6            
 [91] rtracklayer_1.40.3       hwriter_1.3.2            R6_2.2.2                
 [94] latticeExtra_0.6-28      gridExtra_2.3            dichromat_2.0-0         
 [97] MASS_7.3-50              assertthat_0.2.0         Category_2.46.0         
[100] withr_2.1.2              GenomicAlignments_1.16.0 Rsamtools_1.32.2        
[103] GenomeInfoDbData_1.1.0   hms_0.4.2                grid_3.5.1              
[106] rpart_4.1-13             coda_0.19-1              biovizBase_1.28.1       
[109] bbmle_1.0.20             numDeriv_2016.8-1        base64enc_0.1-3      

You don't say what species you are querying, but do note that there isn't a VGNC name or ID for human, because VGNC is for non-human species. If I try say, bovine, I have no problems:

> library(biomaRt)
> mart <- useMart("ensembl","btaurus_gene_ensembl")

> ids <- head(keys(org.Bt.eg.db, "ENSEMBL"))
> ids
[1] "ENSBTAG00000022255" "ENSBTAG00000017280" "ENSBTAG00000037533"
[4] "ENSBTAG00000004371" "ENSBTAG00000007148" "ENSBTAG00000007101"

> grep("gnc", listAttributes(mart)[,1], value = TRUE)
[1] "hgnc_id"         "hgnc_symbol"     "hgnc_trans_name" "vgnc"           
[5] "vgnc_trans_name"
> getBM(c("ensembl_gene_id","vgnc","vgnc_trans_name"), "ensembl_gene_id", ids, mart)
     ensembl_gene_id       vgnc vgnc_trans_name
1 ENSBTAG00000004371 VGNC:27748          CS-201
2 ENSBTAG00000007101 VGNC:28687          F3-201
3 ENSBTAG00000007148 VGNC:28682          F2-201
4 ENSBTAG00000017280 VGNC:26638          C3-201
5 ENSBTAG00000022255 VGNC:26053          AR-201
6 ENSBTAG00000037533                          

Also, what do you mean by

By the way your url retrieves  "404 not found error".?

It's not clear what you mean by 'your url'.