Question: Problem retrieving data from "ENSEMBL_MART_SNP" database
0
gravatar for AROA SUÁREZ VEGA
19 months ago by
AROA SUÁREZ VEGA20 wrote:

Hi all,

I have a problem using "ENSEMBL_MART_SNP". I have a list of 2400 SNPs and I want to find the genes associated to these SNPs using biomart.

When I use the database "ENSEMBL_MART_SNP" with the following commands:

ensembl <- useMart(biomart = "ENSEMBL_MART_SNP", 
                dataset = "btaurus_snp", 
                host = 'www.ensembl.org')

Genes_Biomart<-getBM(attributes=c("refsnp_id","ensembl_gene_stable_id","chr_name","chrom_start","chrom_end"), 
                     filters = "chromosomal_region", 
                     values = positionsBiomart, 
                     mart = ensembl)

I get this error:

Error in getBM(attributes = c("refsnp_id", "ensembl_gene_stable_id", "chr_name",  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

Does anyone knows the solution?

Thank you very much in advance!!

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages:
[1] biomaRt_2.34.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15         AnnotationDbi_1.40.0 xml2_1.2.0           magrittr_1.5        
 [5] BiocGenerics_0.24.0  progress_1.1.2       IRanges_2.12.0       bit_1.1-12          
 [9] R6_2.2.2             rlang_0.2.0          httr_1.3.1           stringr_1.3.0       
[13] blob_1.1.0           tools_3.4.3          parallel_3.4.3       Biobase_2.38.0      
[17] DBI_0.8              bit64_0.9-7          digest_0.6.15        assertthat_0.2.0    
[21] tibble_1.4.2         S4Vectors_0.16.0     bitops_1.0-6         curl_3.1            
[25] RCurl_1.95-4.10      memoise_1.1.0        RSQLite_2.0          stringi_1.1.6       
[29] compiler_3.4.3       BiocInstaller_1.28.0 pillar_1.2.1         prettyunits_1.0.2   
[33] stats4_3.4.3         XML_3.98-1.10    

biomart ensembl • 367 views
ADD COMMENTlink written 19 months ago by AROA SUÁREZ VEGA20
Can you provide some example data for `positionsBiomart` so I can test your code on my computer?
ADD REPLYlink written 19 months ago by Mike Smith4.0k
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