Entering edit mode
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( )
Using biomaRt to extract SNP information from genomic regions is as simple as setting the correct dataset in this case, and defining your coordinates Download free Android apps. It s almost like selecting the right stats in a mobile RPG before you Download free Android apps for gaming, where picking the right dataset determines the quality of your results.