| Bio::PopGen::Genotype(3pm) | User Contributed Perl Documentation | Bio::PopGen::Genotype(3pm) |
Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container
use Bio::PopGen::Genotype;
my $genotype = Bio::PopGen::Genotype->new(-marker_name => $name,
-individual_id => $indid,
-alleles => \@alleles);
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.
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Please direct usage questions or support issues to the mailing list:
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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.
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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 _
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
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
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
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
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.
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
Title : reset_Alleles Usage : $genotype->reset_Alleles; Function: Resets the stored alleles so the list is empty Returns : None Args : None
| 2018-10-27 | perl v5.26.2 |