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Bio::PopGen::Genotype.3pm

NAME

Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container

SYNOPSIS

   use Bio::PopGen::Genotype;
   my $genotype = Bio::PopGen::Genotype->new(-marker_name   => $name,
                                            -individual_id => $indid,
                                            -alleles       => \@alleles);
 
 

DESCRIPTION

This object will contain alleles for a given marker for a given individual.

The class variable BlankAlleles (accessible through $Bio::PopGen::Genotype::BlankAlleles = 'somepattern') can be set to a regexp pattern for identifying blank alleles which should no be counted (they are effectively missing data). By default it set to match white space, '-', 'N' or 'n', and '?' as blank alleles which are skipped.

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 the web:

   http://bugzilla.open-bio.org/
 
 

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 _

new

  Title   : new
  Usage   : my $obj = Bio::PopGen::Genotype->new();
  Function: Builds a new Bio::PopGen::Genotype object 
  Returns : an instance of Bio::PopGen::Genotype
  Args    : -marker_name   => string representing name of the marker
            -individual_id => string representing individual id (optional)
            -alleles       => arrayref with each item in the array being an allele
 
 

marker_name

  Title   : marker_name
  Usage   : my $name = $genotype->marker_name();
  Function: Get the marker name for a genotype result
  Returns : string
  Args    : [optional] marker name value to store
 
 

individual_id

  Title   : individual_id
  Usage   : my $indid = $genotype->individual_id();
  Function: Gets the individual id associated with a genotype
            This is effectively a back reference since we will typically
            associate a genotype with an individual with an 
            individual HAS-A genotype relationship.
  Returns : unique id string for an individual
  Args    : none
 
 

get_Alleles

  Title   : get_Alleles
  Usage   : my @alleles = $genotype->get_Alleles();
  Function: Get the alleles for a given marker and individual
  Returns : array of alleles (strings in this implementation)
  Args    : $showblank - boolean flag to indicate return ALL alleles not 
                         skipping the coded EMPTY alleles
 
  Note    : Uses the class variable $BlankAlleles to test if alleles
            should be skipped or not.
 
 

add_Allele

  Title   : add_Allele
  Usage   : $genotype->add_Allele(@alleles);
  Function: Add alleles to the genotype, at this point there is no
            verification to insure that haploid individuals only have 1 
            allele or that diploids only have 2 - we assume that is
            done by the user creating these objects 
  Returns : count of the number of alleles in genotype
  Args    : Array of alleles to store
 
 

reset_Alleles

  Title   : reset_Alleles
  Usage   : $genotype->reset_Alleles;
  Function: Resets the stored alleles so the list is empty
  Returns : None
  Args    : None