Provided by: libbio-perl-perl_1.6.901-2_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.
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: firstname.lastname@example.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/
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 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