Bio::PopGen Marker
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Summary
Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes
Package variables
No package variables defined.
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
newDescriptionCode
nameDescriptionCode
descriptionDescriptionCode
typeDescriptionCode
unique_idDescriptionCode
annotationDescriptionCode
get_AllelesDescriptionCode
get_Allele_FrequenciesDescriptionCode
add_Allele_FrequencyDescriptionCode
reset_allelesDescriptionCode
marker_coverageDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::PopGen::Marker->new();
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
namecodeprevnextTop
 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
descriptioncodeprevnextTop
 Title   : description
Usage : my $desc = $marker->description
Function: Get the marker description free text
Returns : string
Args : [optional] string
typecodeprevnextTop
 Title   : type
Usage : my $type = $marker->type;
Function: Get coded string for marker type
Returns : string
Args : [optional] string
unique_idcodeprevnextTop
 Title   : unique_id
Usage : my $id = $marker->unique_id;
Function: Get the unique marker ID
Returns : unique ID string
Args : [optional ] string
annotationcodeprevnextTop
 Title   : annotation
Usage : my $annotation_collection = $marker->annotation;
Function: Get/set a Bio::AnnotationCollectionI for this marker
Returns : Bio::AnnotationCollectionI object
Args : [optional set] Bio::AnnotationCollectionI object
get_AllelescodeprevnextTop
 Title   : get_Alleles
Usage : my @alleles = $marker->get_Alleles();
Function: Get the available marker alleles
Returns : Array of strings
Args : none
get_Allele_FrequenciescodeprevnextTop
 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_FrequencycodeprevnextTop
 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_allelescodeprevnextTop
 Title   : reset_alleles
Usage : $marker->reset_alleles();
Function: Reset the alleles for a marker
Returns : None
Args : None
marker_coveragecodeprevnextTop
 Title   : marker_coverage
Usage : $marker->marker_coverage();
Function: Get marker coverage, that is, the number of
individuals where the marker is present
excluding missing or ambiguous alleles
Returns : integer, representing marker coverage
Args :
Methods code
newdescriptionprevnextTop
sub new {
  my($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 provide 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;
}
namedescriptionprevnextTop
sub name {
    my $self = shift;

    return $self->{'_name'} = shift if @_;
    return $self->{'_name'};
}
descriptiondescriptionprevnextTop
sub description {
    my $self = shift;

    return $self->{'_description'} = shift if @_;
    return $self->{'_description'};
}
typedescriptionprevnextTop
sub type {
    my $self = shift;

    return $self->{'_type'} = shift if @_;
    return $self->{'_type'};
}
unique_iddescriptionprevnextTop
sub unique_id {
    my $self = shift;

    return $self->{'_uniqueid'} = shift if @_;
    return $self->{'_uniqueid'};
}
annotationdescriptionprevnextTop
sub annotation {
   my ($self, $arg) = @_;
   return $self->{_annotation} unless $arg;
   $self->throw("Bio::AnnotationCollectionI required for argument") unless
       ref($arg) && $arg->isa('Bio::AnnotationCollectionI');
   return $self->{_annotation} = $arg;
}
get_AllelesdescriptionprevnextTop
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 $a } @alpha;
    return @numeric,@alpha;
}
get_Allele_FrequenciesdescriptionprevnextTop
sub get_Allele_Frequencies {
   return %{$_[0]->{'_allele_freqs'}};
}
add_Allele_FrequencydescriptionprevnextTop
sub add_Allele_Frequency {
   my ($self,$allele,$freq) = @_;
   $self->{'_allele_freqs'}->{$allele} = $freq;
}
reset_allelesdescriptionprevnextTop
sub reset_alleles {
   my ($self) = @_;
   $self->{'_allele_freqs'} = {};
}
marker_coveragedescriptionprevnextTop
sub marker_coverage {
    my ($self) = @_;
 
    return $self->{_marker_coverage};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason-at-bioperl.org
CONTRIBUTORSTop
Matthew Hahn, matthew.hahn-at-duke.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _