Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes 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 object will not contain genotype information pertaining to an individual, but rather population level statistics and descriptive information about a marker.

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/MailList.shtml - About the mailing lists

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: http://bugzilla.bioperl.org/ Email jason-at-bioperl.org 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 = new Bio::PopGen::Marker(); Function: Builds a new Bio::PopGen::Marker object Returns : an instance of Bio::PopGen::Marker Args : -name => [string] marker name -description => [string] marker description -type => [string] marker type -unique_id => [string/int] unique id -allele_freq => [hash ref] allele frequencies

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

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

get_Alleles
Title : get_Alleles Usage : my @alleles = $marker->get_Alleles(); Function: Get the available marker alleles 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 where keys are the names of the alleles Args : none

add_Allele_Frequency
Title : add_Allele_Frequency Usage : $marker->add_Allele_Frequency($allele,$freq) Function: Adds an allele frequency Returns : None Args : $allele - allele name $freq - frequency value

reset_alleles
Title : reset_alleles Usage : $marker->reset_alleles(); Function: Reset the alleles for a marker Returns : None Args : None