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.\" ========================================================================
.\"
.IX Title "Bio::PopGen::Marker 3pm"
.TH Bio::PopGen::Marker 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::PopGen::Marker \- A genetic marker which one uses to generate genotypes
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 8
\&  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
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object will not contain genotype information pertaining to an
individual, but rather population level statistics and descriptive
information about a marker.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Matthew Hahn, matthew.hahn\-at\-duke.edu
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 9
\& 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
.Ve
.SS "name"
.IX Subsection "name"
.Vb 5
\& 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
.Ve
.SS "description"
.IX Subsection "description"
.Vb 5
\& Title   : description
\& Usage   : my $desc = $marker\->description
\& Function: Get the marker description free text
\& Returns : string
\& Args    : [optional] string
.Ve
.SS "type"
.IX Subsection "type"
.Vb 5
\& Title   : type
\& Usage   : my $type = $marker\->type;
\& Function: Get coded string for marker type
\& Returns : string
\& Args    : [optional] string
.Ve
.SS "unique_id"
.IX Subsection "unique_id"
.Vb 5
\& Title   : unique_id
\& Usage   : my $id = $marker\->unique_id;
\& Function: Get the unique marker ID
\& Returns : unique ID string
\& Args    : [optional ] string
.Ve
.SS "annotation"
.IX Subsection "annotation"
.Vb 5
\& 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
.Ve
.SS "get_Alleles"
.IX Subsection "get_Alleles"
.Vb 5
\& Title   : get_Alleles
\& Usage   : my @alleles = $marker\->get_Alleles();
\& Function: Get the available marker alleles
\& Returns : Array of strings
\& Args    : none
.Ve
.SS "get_Allele_Frequencies"
.IX Subsection "get_Allele_Frequencies"
.Vb 8
\& 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
.Ve
.SS "add_Allele_Frequency"
.IX Subsection "add_Allele_Frequency"
.Vb 6
\& 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
.Ve
.SS "reset_alleles"
.IX Subsection "reset_alleles"
.Vb 5
\& Title   : reset_alleles
\& Usage   : $marker\->reset_alleles();
\& Function: Reset the alleles for a marker
\& Returns : None
\& Args    : None
.Ve
.SS "marker_coverage"
.IX Subsection "marker_coverage"
.Vb 7
\& Title   : marker_coverage
\& Usage   : $marker\->marker_coverage();
\& Function: Get marker coverage, that is, the number of 
\&           individuals where the marker is present 
\&           excluding missing or ambiguous alleles
\& Returns : integer, representing marker coverage
\& Args    :
.Ve