Provided by: libbio-perl-perl_1.6.923-1_all
Bio::PopGen::MarkerI - A Population Genetic conceptual marker
# 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
This is the basic interface for Markers which one can associate alleles with for calculating Theta and Pi.
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 email or 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 _ 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