[ensembl-dev] Ld scores from ensembl

[Nathalie Conte]

Hi
I am trying to get LD scores from slice, I am using the tutorial script from ensembl
http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ld

I retrieve data with 79, not with 80
any idea of why?
thanks
Nathalie

#!/usr/local/bin/perl
use strict;
use warnings;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    -host=>"ensembldb.ensembl.org", -user=>"anonymous",
    -port=>'5306', 'db_version' => 80,);
my $chr = 6;  #defining the region in chromosome 6
my $start = 25_834_000;
my $end = 25_854_000;


my $population_name = 'CSHL-HAPMAP:HapMap-CEU'; #we only want LD in this population
#my $population_name ='1000GENOMES:phase_3:CEU'; # I also tried with this population

my $slice_adaptor = $registry->get_adaptor('human', 'core', 'slice'); #get adaptor for Slice object
my $slice = $slice_adaptor->fetch_by_region('chromosome',$chr,$start,$end); #get slice of the region

my $population_adaptor = $registry->get_adaptor('human', 'variation', 'population'); #get adaptor for Population object
my $population = $population_adaptor->fetch_by_name($population_name); #get population object from database

my $ldFeatureContainerAdaptor = $registry->get_adaptor('human', 'variation', 'ldfeaturecontainer'); #get adaptor for LDFeatureContainer object
my $ldFeatureContainer = $ldFeatureContainerAdaptor->fetch_by_Slice($slice,$population); #retrieve all LD values in the region


foreach my $r_square (@{$ldFeatureContainer->get_all_r_square_values}){
  if ($r_square->{r2} > 0.8){ #only print high LD, where high is defined as r2 > 0.8
    print "High LD between variations ", $r_square->{variation1}->variation_name,"-", $r_square->{variation2}->variation_name, "\n";
  }
}
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