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')
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!!
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
 LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252
 LC_NUMERIC=C LC_TIME=Spanish_Spain.1252
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
loaded via a namespace (and not attached):
 Rcpp_0.12.15 AnnotationDbi_1.40.0 xml2_1.2.0 magrittr_1.5
 BiocGenerics_0.24.0 progress_1.1.2 IRanges_2.12.0 bit_1.1-12
 R6_2.2.2 rlang_0.2.0 httr_1.3.1 stringr_1.3.0
 blob_1.1.0 tools_3.4.3 parallel_3.4.3 Biobase_2.38.0
 DBI_0.8 bit64_0.9-7 digest_0.6.15 assertthat_0.2.0
 tibble_1.4.2 S4Vectors_0.16.0 bitops_1.0-6 curl_3.1
 RCurl_1.95-4.10 memoise_1.1.0 RSQLite_2.0 stringi_1.1.6
 compiler_3.4.3 BiocInstaller_1.28.0 pillar_1.2.1 prettyunits_1.0.2
 stats4_3.4.3 XML_3.98-1.10