I have a list of 150 locations (eg: "10:112834:113150") and I would like to retrieve the variants found in these locations,
This is the command I use to get the variants (fantom_locs contains the list of locations):
snp_db <- useEnsembl(biomart="snp", dataset="hsapiens_snp") snps_FANTOM <- getBM(attributes = c('refsnp_id'), filters = c('chromosomal_region'), values = fantom_locs, mart = snp_db)
It works for a few locations but then I get a timeout error, I can implement a for loop to fetch the snps on one location at a time, but it is very slow and I just wondered if there was a better way to do this.
For example is it worth it to download a local version of the mart ?