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Hi Catherine<br>
<br>
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.<br>
<br>
All the best<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 20/02/2015 13:32, Catherine Leroy
wrote:<br>
</div>
<blockquote
cite="mid:D073601E-A2C7-4B25-931B-8E33DEA263EC@ebi.ac.uk"
type="cite">
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charset=windows-1252">
Hello,
<div><br>
</div>
<div>I am trying to work my head around LD. As you might see from
my questions it is all quite new to me.</div>
<div><br>
</div>
<div>I have the following snp : <span style="background-color:
rgb(255, 255, 255);">rs11010067</span></div>
<div><span style="background-color: rgb(255, 255, 255);">and I am
trying to get the r2 value using the script I’ve copied past
below.</span></div>
<div><span style="background-color: rgb(255, 255, 255);"><br>
</span></div>
<div><span style="background-color: rgb(255, 255, 255);">If I
enter as population : Europe </span></div>
<div><span style="background-color: rgb(255, 255, 255);">then I
don’t get anything back. </span></div>
<div><span style="background-color: rgb(255, 255, 255);"><br>
</span></div>
<div><span style="background-color: rgb(255, 255, 255);">If I
enter as population : </span><span style="background-color:
rgb(255, 255, 255);">CSHL-HAPMAP:HapMap-CEU</span></div>
<div>
<div>Then I get back a list of variation1, variation2 and r2. </div>
</div>
<div><br>
</div>
<div>I don’t understand why I don’t get anything with Europe. </div>
<div>Could somebody explain that to me or point me to some
documentation about LD I could read. </div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>Thanks for your help,</div>
<div>Catherine</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<pre style="background-color: rgb(255, 255, 255);"><font face="Helvetica">use strict;
use warnings;
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => '<a moz-do-not-send="true" href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a>',
-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'); <span style="font-style: italic;">#get adaptor for Population object
</span>my $population = $population_adaptor->fetch_by_name("CSHL-HAPMAP:HapMap-CEU");
<span style="font-style: italic;">#my $population = $population_adaptor->fetch_by_name("Europe");
</span><span style="font-style: italic;">
</span>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'); <span style="font-style: italic;">#get adaptor for LDFeatureContainer object
</span><span style="font-style: italic;"> </span>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 = $variation_feature_1->name();
<span style="font-style: italic;">#$variation1
</span><span style="font-style: italic;"> </span>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";
}
}
</font></pre>
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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 </pre>
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