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.