I'd like to gather the genotype frequency for a number of snps for HSapiens in R using BioMart. As far as I understand, the best way to do this is via ensembl through useEnsembl(biomart="snp")
From there however, the hsapiens_snp
dataset, which I assume is the main one, doesn't contain any genotype frequency in the listAttributes
. The dataset hsapiens_snp_som
however does contain genotype frequency, but the number of snps it contains is very small it seems in comparison to the hsapiens_snp
dataset (only 41kb in size vs 400kb for hsapiens_snp
).
Would anyone know how I could obtain genotype frequency in R using biomart, for snps? Thanks.
Thanks Emily. I've installed the Perl API, but cannot see instructions anywhere to pull actual genotype frequency data.