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

NAME

       Bio::PopGen::MarkerI - A Population Genetic conceptual marker

SYNOPSIS

       # Get a Bio::PopGen::MarkerI somehow - like using a Bio::PopGen::Marker

	 my $name = $marker->name();		# marker name
	 my $description = $marker->description(); # description
	 my $type = $marker->type();		# coded type of the marker
	 my $unique_id = $marker->unique_id;	# optional unique ID

	 my @alleles = $marker->get_Alleles();	# the known alleles
	 my %allele_freqs = $marker->get_Allele_Frequencies(); # keys are marker names
						# vals are frequencies
						# may change to handle multiple populations

DESCRIPTION

       This is the basic interface for Markers which one can associate alleles with for calculating Theta and Pi.

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
       email or 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 _

   name
	Title	: name
	Usage	: my $name = $marker->name();
	Function: Get the name of the marker
	Returns : string representing the name of the marker
	Args	:

   description
	Title	: description
	Usage	: my $desc = $marker->description
	Function: Get the marker description free text
	Returns : string
	Args	: [optional] string

   type
	Title	: type
	Usage	: my $type = $marker->type;
	Function: Get coded string for marker type
	Returns : string
	Args	: [optional] string

   unique_id
	Title	: unique_id
	Usage	: my $id = $marker->unique_id;
	Function: Get the unique marker ID
	Returns : unique ID string
	Args	: [optional ] string

   annotation
	Title	: annotation
	Usage	: $obj->annotation($seq_obj)
	Function: retrieve the attached annotation object
	Returns : Bio::AnnotationCollectionI or none;

       See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information. This method comes through extension from
       Bio::AnnotatableI.

   get_Alleles
	Title	: get_Alleles
	Usage	: my @alleles = $marker->get_Alleles();
	Function: Get the available marker alleles if they are known and stored
	Returns : Array of strings
	Args	: none

   get_Allele_Frequencies
	Title	: get_Allele_Frequencies
	Usage	: my %allele_freqs = $marker->get_Allele_Frequencies;
	Function: Get the alleles and their frequency (set relative to
		  a given population - you may want to create different
		  markers with the same name for different populations
		  with this current implementation
	Returns : Associative array (hash) where keys are the names of the alleles
	Args	: none

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