[ensembl-dev] LD/population questions

[Catherine Leroy]

I get my snp and ethnicity from the gwas catalog database. The specific example I gave earlier is pubmed : 23128233. So I won’t have much more then what I have put in my script. 
So there’s no such thing as r2 data for ‘European population’?

 
On 20 Feb 2015, at 14:36, Emily Perry <emily at ebi.ac.uk> wrote:

> Hi Catherine
> 
> You need to use the names that the populations are called in the database, so to get 1000 genomes Europeans you would use 1000GENOMES:phase_1_EUR.
> 
> All the best
> 
> Emily
> 
> On 20/02/2015 13:32, Catherine Leroy wrote:
>> Hello, 
>> 
>> I am trying to work my head around LD. As you might see from my questions it is all quite new to me.
>> 
>> I have the following snp : rs11010067
>> and I am trying to get the r2 value using the script I’ve copied past below.
>> 
>> If I enter as population : Europe 
>> then I don’t get anything back. 
>> 
>> If I enter as population : CSHL-HAPMAP:HapMap-CEU
>> Then I get back a list of variation1, variation2 and r2. 
>> 
>> I don’t understand why I don’t get anything with Europe. 
>> Could somebody explain that to me or point me to some documentation about LD I could read. 
>> 
>> I would want to use r2 to determine if a snp I have is in the same LD Block then the gene I’m supposing it is linked to using a threshold for r2 (which I haven’t determine yet, I’ve just started working on that). The problem is that the indication I have as population for this snp in my data (Gwas catalog) is Europe which doesn’t return anything. 
>> 
>> Thanks for your help,
>> Catherine
>> 
>> 
>> 
>> 
>> use strict;
>> use warnings;
>> use Bio::EnsEMBL::Registry;
>> 
>> 
>> my $registry = 'Bio::EnsEMBL::Registry';
>> 
>> $registry->load_registry_from_db(
>> -host   => 'ensembldb.ensembl.org',
>> -user   => 'anonymous',
>> );
>> 
>> my $rs_id = "rs11010067";
>> 
>> my $variation_adaptor = $registry->get_adaptor( 'human', 'variation', 'variation' );
>> my $variation = $variation_adaptor->fetch_by_name($rs_id);
>> 
>> my $population_adaptor = $registry->get_adaptor('human', 'variation', 'population'); #get adaptor for Population object
>> my $population = $population_adaptor->fetch_by_name("CSHL-HAPMAP:HapMap-CEU");
>> #my $population = $population_adaptor->fetch_by_name("Europe");
>> 
>> foreach my $variation_feature (@{$variation->get_all_VariationFeatures()}) {
>>     print $variation_feature->seq_region_name(),':', $variation_feature->seq_region_start(), '-', $variation_feature->seq_region_end(),"\n";
>> 
>>     my $ldFeatureContainerAdaptor = $registry->get_adaptor('human', 'variation', 'ldfeaturecontainer'); #get adaptor for LDFeatureContainer object
>>     my $ldFeatureContainer = $ldFeatureContainerAdaptor->fetch_by_VariationFeature($variation_feature, $population);
>> 
>>     my $r_square_values = $ldFeatureContainer->get_all_r_square_values();
>>     foreach my $r_square_value (@{$r_square_values}){
>> 
>>         my $variation_feature_1 = $r_square_value->{variation1};
>>         my $variation1_name = $variation_feature_1->name();
>>         #$variation1
>>         my $variation_feature_2 = $r_square_value->{variation2};
>>         my $variation2_name = $variation_feature_2->name();
>> 
>>         my $r2 = $r_square_value->{r2};
>> 
>>         print "variation1 = " , $variation1_name, "variation1_region_name = ", $variation1_name, " \n";
>>         print "variation2 = " , $variation2_name, "variation2_region_name = ", $variation2_name, " \n";
>>         print "r2 = " , $r2 , "\n\n";
>> 
>>     }
>> }
>> 
>> 
>> 
>> 
>> 
>> 
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> 
> -- 
> Dr Emily Perry (Pritchard)
> Ensembl Outreach Officer
> 
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> UK 
> _______________________________________________
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