Reference

Bio::PopGen::Genotype(3pm)

An implementation of GenotypeI which is just an allele container

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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:

  https://github.com/bioperl/bioperl-live/issues

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

marker_type

 Title   : marker_type
 Usage   : my $name = $genotype->marker_type();
 Function: Get the marker type for a genotype result
 Returns : M (microsatellite, or other multi-allelic 
           locus) or S (biallelic/SNP locus)
 Args    : [optional] marker type 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

History