[ensembl-dev] LD/population questions

[Emily Perry]

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  <http://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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