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bio::popgen::marker(3pm) [debian man page]

Bio::PopGen::Marker(3pm)				User Contributed Perl Documentation				  Bio::PopGen::Marker(3pm)

Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes SYNOPSIS
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 DESCRIPTION
This object will not contain genotype information pertaining to an individual, but rather population level statistics and descriptive information about a marker. 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. - General discussion - About the mailing lists Support Please direct usage questions or support issues to the mailing list: 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: AUTHOR - Jason Stajich Email CONTRIBUTORS
Matthew Hahn, 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::Marker->new(); Function: Builds a new Bio::PopGen::Marker object Returns : an instance of Bio::PopGen::Marker Args : -name => [string] marker name -description => [string] marker description -type => [string] marker type -unique_id => [string/int] unique id -allele_freq => [hash ref] allele frequencies name Title : name Usage : my $name = $marker->name(); Function: Get the name of the marker Returns : string representing the name of the marker Args : [optional] name description Title : description Usage : my $desc = $marker->description Function: Get the marker description free text Returns : string Args : [optional] string type Title : type Usage : my $type = $marker->type; Function: Get coded string for marker type Returns : string Args : [optional] string unique_id Title : unique_id Usage : my $id = $marker->unique_id; Function: Get the unique marker ID Returns : unique ID string Args : [optional ] string annotation Title : annotation Usage : my $annotation_collection = $marker->annotation; Function: Get/set a Bio::AnnotationCollectionI for this marker Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object get_Alleles Title : get_Alleles Usage : my @alleles = $marker->get_Alleles(); Function: Get the available marker alleles Returns : Array of strings Args : none get_Allele_Frequencies 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 where keys are the names of the alleles Args : none add_Allele_Frequency Title : add_Allele_Frequency Usage : $marker->add_Allele_Frequency($allele,$freq) Function: Adds an allele frequency Returns : None Args : $allele - allele name $freq - frequency value reset_alleles Title : reset_alleles Usage : $marker->reset_alleles(); Function: Reset the alleles for a marker Returns : None Args : None perl v5.14.2 2012-03-02 Bio::PopGen::Marker(3pm)
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