Genotype Frequency from Ensembl BiomaRt

Question

[mass2]

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.

Answer 1

[Emily]

Genotype frequencies are not available in BioMart. To get genotype frequencies you'd be looking at using the Perl API.

[mass2]

Thanks Emily. I've installed the Perl API, but cannot see instructions anywhere to pull actual genotype frequency data.

Answer 2

[entheologist33]

I need to do this too, I have installed the ensembl Perl API but it only allows me to get allele frequencies, I can't figure out how to get genotype frequencies. Does anyone know how to get genotype frequencies for specific SNPs?

Answer 3

[entheologist33]

The solution has been posted here: Ensembl Perl API - How to get genotype frequencies