[ensembl-dev] Linkage disequilibrium clustering

[Will McLaren]

Hello,

The LDFeatureContainer and adaptor should help you here, see
http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ld

The tutorial has a guide for fetching via a slice (a genomic region), but
you can also fetch LD blocks around a VariationFeature object, see the full
API docs:

http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1LDFeatureContainerAdaptor.html

Mike, I'm afraid there isn't a method to retrieve LD between an arbitrary
pair of variants. The two main methods mentioned above are locus based, ie
they will only retrieve LD values between pairs of variants within a set
distance of each other.

There's absolutely no technical reason why you couldn't have a method to do
the calculation between any two arbitrary variants though; we will look
into adding it to the API.

Regards

Will McLaren
Ensembl Variation

On 2 October 2014 14:37, Mike Pierce <mikepierce2000 at gmail.com> wrote:

> A related question, is there a function that calculates/returns LD for a
> pair of variants in a specific population?
>
> Because you can use that to calculate a relationship matrix and do your
> own clustering.
>
> Mike
>
> On 2 October 2014 14:22, Genomeo Dev <genomeodev at gmail.com> wrote:
>
>> Hi,
>>
>> I have a list of SNPs which I want to cluster into Linkage disequilibrium
>> blocks assuming European ancestry. I was wondering whether there is a quick
>> way to do that using Ensembl variation API?
>>
>> Thanks!
>>
>> --
>> G.
>>
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