Bio::PopGen::Genotype(3pm)				User Contributed Perl Documentation				Bio::PopGen::Genotype(3pm)

NAME

       Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container

SYNOPSIS

	 use Bio::PopGen::Genotype;
	 my $genotype = Bio::PopGen::Genotype->new(-marker_name   => $name,
						  -individual_id => $indid,
						  -alleles	 => @alleles);

DESCRIPTION

       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.

FEEDBACK

   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.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.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
       Email jason-at-bioperl.org

CONTRIBUTORS

       Matthew Hahn, matthew.hahn-at-duke.edu

APPENDIX

       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

perl v5.14.2							    2012-03-02						Bio::PopGen::Genotype(3pm)