Provided by: libbio-perl-perl_1.6.923-1_all
Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container
use Bio::PopGen::Genotype; my $genotype = Bio::PopGen::Genotype->new(-marker_name => $name, -individual_id => $indid, -alleles => \@alleles);
This object will contain alleles for a given marker for a given individual. The class variable BlankAlleles (accessible through $Bio::PopGen::Genotype::BlankAlleles = 'somepattern') can be set to a regexp pattern for identifying blank alleles which should no be counted (they are effectively missing data). By default it set to match white space, '-', 'N' or 'n', and '?' as blank alleles which are skipped.
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AUTHOR - Jason Stajich
Matthew Hahn, matthew.hahn-at-duke.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::PopGen::Genotype->new(); Function: Builds a new Bio::PopGen::Genotype object Returns : an instance of Bio::PopGen::Genotype Args : -marker_name => string representing name of the marker -individual_id => string representing individual id (optional) -alleles => arrayref with each item in the array being an allele marker_name Title : marker_name Usage : my $name = $genotype->marker_name(); Function: Get the marker name for a genotype result Returns : string Args : [optional] marker name value to store marker_type Title : marker_type Usage : my $name = $genotype->marker_type(); Function: Get the marker type for a genotype result Returns : M (microsatellite, or other multi-allelic locus) or S (biallelic/SNP locus) Args : [optional] marker type value to store individual_id Title : individual_id Usage : my $indid = $genotype->individual_id(); Function: Gets the individual id associated with a genotype This is effectively a back reference since we will typically associate a genotype with an individual with an individual HAS-A genotype relationship. Returns : unique id string for an individual Args : none get_Alleles Title : get_Alleles Usage : my @alleles = $genotype->get_Alleles(); Function: Get the alleles for a given marker and individual Returns : array of alleles (strings in this implementation) Args : $showblank - boolean flag to indicate return ALL alleles not skipping the coded EMPTY alleles Note : Uses the class variable $BlankAlleles to test if alleles should be skipped or not. add_Allele Title : add_Allele Usage : $genotype->add_Allele(@alleles); Function: Add alleles to the genotype, at this point there is no verification to insure that haploid individuals only have 1 allele or that diploids only have 2 - we assume that is done by the user creating these objects Returns : count of the number of alleles in genotype Args : Array of alleles to store reset_Alleles Title : reset_Alleles Usage : $genotype->reset_Alleles; Function: Resets the stored alleles so the list is empty Returns : None Args : None