[ensembl-dev] Linkage disequilibrium clustering

[Genomeo Dev]

Thanks Will. I have actually just found this, it may actually do exactly
that pairwise calculation:

public Float Bio::EnsEMBL::Variation::LDFeatureContainer::get_r_square()

    Arg [1]     : Bio::EnsEMBL::Variation::VariationFeature
<http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html>
$variationFeature
    Arg [2]     : Bio::EnsEMBL::Variation::VariationFeature
<http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html>
$variationFeature
    Arg [3]     : (optional) int - population_id of population you
want to get the r_square value
    Example     :

 $r_square = $obj->get_r_square($vf1,$vf2,$population_id);

    Description : Get the r_square value for a pair of variation
features in the given population. If no population is provided,
    return the r_square for the default population with more sample
counts (in case more than 1)
    ReturnType  : float
    Exceptions  : throw on incorrect arguments
    Caller      : general
    Status      : At Risk


On 2 October 2014 14:43, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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.
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>


-- 
G.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20141002/c88d4ccb/attachment.html>