Summary

Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes

Package variables

Included modules

Inherit

Bio::PopGen::MarkerI Bio::Root::Root

Synopsis

  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 object will not contain genotype information pertaining to an
individual, but rather population level statistics and descriptive
information about a marker.

Methods

Methods description

 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

 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

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

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

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

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

 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

 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

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

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($name,$desc,$type,$uid,$af) = $self->_rearrange([qw(NAME
							  DESCRIPTION
							  TYPE
							  UNIQUE_ID
							  ALLELE_FREQ)],@args);
  $self->{'_allele_freqs'} = {};
  if( ! defined $uid ) {
      $uid = $UniqueCounter++;
  }
  if( defined $name) {
      $self->name($name);
  } else { 
      $self->throw("Must have provided a name when initializing a Marker");
  }
  defined $desc && $self->description($desc);
  defined $type && $self->type($type);
  $self->unique_id($uid);
  if( defined $af) {
      if( ref($af) !~ /HASH/i ) {
	  $self->warn("Must provide valid Hash reference for allele_freq method");
      } else { 
	  foreach my $allele ( keys %$af ) {
	      $self->add_Allele_Frequency($allele, $af->{$allele});
	  }
      }
  }
  return $self;

}

sub name {

    my $self = shift;

    return $self->{'_name'} = shift if @_;
    return $self->{'_name'};

}

sub description {

    my $self = shift;

    return $self->{'_description'} = shift if @_;
    return $self->{'_description'};

}

sub type {

    my $self = shift;

    return $self->{'_type'} = shift if @_;
    return $self->{'_type'};

}

sub unique_id {

    my $self = shift;

    return $self->{'_uniqueid'} = shift if @_;
    return $self->{'_uniqueid'};

}

sub get_Alleles {

    my $self = shift;
    my (@numeric,@alpha);
    
    for ( keys %{$self->{'_allele_freqs'}} ) {
	if( /[^\d\.\-e]/ ) { push @alpha, $_ }
	else { push @numeric, $_ }
    }
    @numeric = sort { $b <=> $a } @numeric;
    @alpha   = sort { $b cmp $a } @alpha;
    return @numeric,@alpha;

}

sub get_Allele_Frequencies {

   return %{$_[0]->{'_allele_freqs'}};

}

sub add_Allele_Frequency {

   my ($self,$allele,$freq) = @_;
   $self->{'_allele_freqs'}->{$allele} = $freq;

}

sub reset_alleles {

   my ($self) = @_;
   $self->{'_allele_freqs'} = {};

}

General documentation

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

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 _