NAME

Genetics::SNP


SYNOPSIS

  $snp = new Genetics::SNP(name => 'EAEx1.1',
                           importID => 265,
                           dateCreated => $today,
                           Keywords => [ {name => "Test Data", 
                                          dataType => "Boolean", 
                                          value => 1},
                                       ], 
                           chromosome => "12", 
                           malePloidy => 2,
                           femalePloidy => 2,
                           snpType => "Substitution",
                           functionClass => "Synonymous",
                           snpIndex => 2,
                           isConfirmed => 1,
                           confirmMethod => "Resequencing",
                           comment => "Highly expressed in muscle",
                           Organism => {genusSpecies => "Homo sapiens"},
                           Alleles => [ {name => "C", type => "Nucleotide"}, 
                                        {name => "T", type => "Nucleotide"} ],
                           Sequence => {lengthUnits => "bp",
                                        length => 17,
                                        sequence => "ACGTUMRWSYKVHDBXN"},
                           ISCNMapLocations => [ {chrNumber => "12", 
                                                  chrArm => "p", 
                                                  band => "12.2", 
                                                  bandingMethod => "Geimsa"}, 
                                               ],
                          ) ;

See the GenPerl Tutorial for more information.


DESCRIPTION

SNP objects represent single nucleotide polymorphisms.


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

getSequence

 Function  : Return the nucleotide sequence of a SNP object
 Arguments : N/A
 Returns   : A scalar text string
 Example   : getSequence()
 Scope     : Public Instance Method
 Comments  :

printXML

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

asHTML

  Function  : Generate an HTML representation of the object.
  Argument  : A Genetics::SNP object and a scalar containing the name of the 
              GenPerl database in which the object is stored. 
  Returns   : Scalar containing the HTML text.
  Scope     : Public Instance Method
  Comments  : Calls Genetics::Object->_generalHTMLParam to generate HTML 
              elements common to all Genetics::Object objects.  An 
              HTML::Template object is used to actually generate the HTML.