Bio::PopGen::Genotype(3pm) User Contributed Perl Documentation 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:
https://redmine.open-bio.org/projects/bioperl/
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
perl v5.14.2 2012-03-02 Bio::PopGen::Genotype(3pm)