[ensembl-dev] Linkage disequilibrium clustering

[Will McLaren]

That method only retrieves values that have been calculated already.

When you fetch an LDFeatureContainer from the adaptor, the LD values are
precalculated for the relevant Slice or VariationFeature; all the methods
on the LDFeatureContainer apply only to retrieving these results.

Will

On 2 October 2014 15:09, Genomeo Dev <genomeodev at gmail.com> wrote:

> 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.
>>>>
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>>>
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>>
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>>
>
>
> --
> G.
>
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