FrequencySource.pm

- NAME
- SYNOPSIS
- DESCRIPTION
- LICENSE
- FEEDBACK
- AUTHOR - Steve Mathias
- DETAILS
- Imported Packages
- Public methods

- getAlleleFreqsByMarkerName
- printXML

# NAME

Genetics::FrequencySource

# SYNOPSIS

      $fs = new Genetics::FrequencySource(name => 'WICGR SNP Freqs',
                                          importID => 270,
                                          dateCreated => $today,
                                          Keywords => [ {name => "Test Data",
                                                         dataType => "Boolean",
                                                         value => 1},
                                                      ],
                                          ObsAlleleFrequencies => [ {Allele => {Marker => {name => "EAEx1.1",
                                                                                           importID => 265},
                                                                                name => "T",
                                                                                type => "nucleotide"},
                                                                     frequency => "0.64",
                                                                    },
                                                                    {Allele => {Marker => {name => "EAEx1.1",
                                                                                           importID => 265},
                                                                                name => "C",
                                                                                type => "nucleotide"},
                                                                     frequency => "0.36",
                                                                    }
                                                                  ],
                                          ObsHtFrequencies => [ {Haplotype => {name => '12pEA1.2',
                                                                               importID => 269,},
                                                                 frequency => 1.00,
                                                                }
                                                              ]
                                         ) ;

    See the GenPerl Tutorial for more information.

# DESCRIPTION

FrequencySource objects represent the allele and/or haplotype frequencies in a particular group of Subjects not represented in the database.

# LICENSE

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

# FEEDBACK

Currently, all feedback should be sent directly to the author.

# AUTHOR - Steve Mathias

Email: mathias@genomica.com

Phone: (720) 565-4029

Address: Genomica Corporation 1745 38th Street Boulder, CO 80301

# DETAILS

The rest of the documentation describes each of the object variables and methods. The names of internal variables and methods are preceded with an underscore (_).

# Imported Packages

     Genetics::Object       Superclass
     strict                 Just to be anal
     vars                   Global variables

# Public methods

## getAlleleFreqsByMarkerName

      Function  : Return allele frequencies for an individual marker.
      Argument  : A Marker object and a string containing an allele type.
      Returns   : Hash reference to a hash with the following structure:
                    $freqs{AlleleName} = $number
      Scope     : Public
      Comments  : This method requires that Markers are uniquely named within the
                  FrequencySource.

## printXML

      Function  : Print an XML representation of the object.
      Argument  : An XML::Writer object being used to generate the XML.
      Returns   : String
      Scope     : Public Instance Method
      Comments  : Calls Genetics::Object->printGeneralXML to generate XML elements
                  common to all Genetics::Object objects.