| Bio::PopGen::MarkerI(3pm) | User Contributed Perl Documentation | Bio::PopGen::MarkerI(3pm) |
Bio::PopGen::MarkerI - A Population Genetic conceptual marker
# Get a Bio::PopGen::MarkerI somehow - like using a Bio::PopGen::Marker
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
This is the basic interface for Markers which one can associate alleles with for calculating Theta and Pi.
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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.
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 email or the web:
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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 : name Usage : my $name = $marker->name(); Function: Get the name of the marker Returns : string representing the name of the marker Args :
Title : description Usage : my $desc = $marker->description Function: Get the marker description free text Returns : string Args : [optional] string
Title : type Usage : my $type = $marker->type; Function: Get coded string for marker type Returns : string Args : [optional] string
Title : unique_id Usage : my $id = $marker->unique_id; Function: Get the unique marker ID Returns : unique ID string Args : [optional ] string
Title : annotation Usage : $obj->annotation($seq_obj) Function: retrieve the attached annotation object Returns : Bio::AnnotationCollectionI or none;
See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information. This method comes through extension from Bio::AnnotatableI.
Title : get_Alleles Usage : my @alleles = $marker->get_Alleles(); Function: Get the available marker alleles if they are known and stored Returns : Array of strings Args : none
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 (hash) where keys are the names of the alleles
Args : none
| 2018-10-27 | perl v5.26.2 |