Extract snp information from genomic regions with biomaRt -> "oaries_snp"
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Jesus • 0
@e3fd7b47
Last seen 15 days ago
Spain

R code:

snpmart = useEnsembl(biomart = "ENSEMBL_MART_SNP", dataset="oaries_snp", host="https://www.ensembl.org")
attributes = listAttributes(snpmart) ## to show name of all possibilities
## list the available datasets in this Mart
listFilters(mart = snpmart)

getBM(attributes = c("refsnp_id", "allele", "chrom_start", "chrom_end", "chrom_strand"),
  filters = "chromosomal_region",
  values = "15:30653960:30653960:1",
  mart = snpmart)



Error en .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, : 
  Query ERROR: caught BioMart::Exception::Configuration: returning undef ... missing filters from your importable?

However, there is this information:
getBM(attributes = c('refsnp_id', 'allele', 'chrom_start', 'chrom_end', "chrom_strand"),
      filters = c('snp_filter'), 
      values = c("rs411068220"),
      mart = snpmart)

"    refsnp_id allele chrom_start chrom_end chrom_strand
1 rs411068220    A/G    30653960  30653960            1"

sessionInfo( )
biomaRt • 113 views
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