Genotype Frequency from Ensembl BiomaRt
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Entering edit mode
6.2 years ago
mass2 • 0

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.

biomart • 2.3k views
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Entering edit mode
6.2 years ago

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

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

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6.1 years ago

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?

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6.1 years ago

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

 

 

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