Genetics::StudyVariable
$sv = new Genetics::StudyVariable(name => 'EA Aff Stat', importID => 445, dateCreated => $today, Keywords => [ {name => "Test Data", dataType => "Boolean", value => 1}, ], description => "EA Trait Locus", category => "AffectionStatus", format => "Code", isXLinked => 0, Codes => [ {code => 0, description => "Unknown EA Status"}, {code => 1, description => "EA Unaffected"}, {code => 2, description => "EA Affected"}, ], AffStatDef => {name => 'EA', diseaseAlleleFreq => 0.001, pen11 => 0.0, pen12 => 0.0, pen22 => 1.0, AffStatElements => [ {code => 0, type => "Unknown", formula => "'EA Aff Stat' = 0"}, {code => 1, type => "Unaffected", formula => "'EA Aff Stat' = 1"}, {code => 2, type => "Affected", formula => "'EA Aff Stat' = 2"}, ], }, LCDef => {name => 'EA Default LC', LiabilityClasses => [ {code => 0, description => "Unknown Age", pen11 => 0.0, pen12 => 0.0, pen22 => 1.0, formula => "'Age' = ''"}, {code => 1, description => "Age less than 40", pen11 => 0.0, pen12 => 0.2, pen22 => 1.0, formula => "'Age' < 40"}, {code => 2, description => "Age less than 50", pen11 => 0.0, pen12 => 0.3, pen22 => 1.0, formula => "'Age' < 50"}, {code => 3, description => "Age grater than or equal to 60", pen11 => 0.0, pen12 => 0.4, pen22 => 1.0, formula => "'Age' >= 60"}, ], }, ) ;
See the GenPerl Tutorial for more information.
StudyVariable objects represent definitions of physical traits, affection status loci, environmental exposure, or drug treatments.
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
Currently, all feedback should be sent directly to the author.
Email: mathias@genomica.com
Phone: (720) 565-4029
Address: Genomica Corporation 1745 38th Street Boulder, CO 80301
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 (_).
Genetics::Object Superclass strict Just to be anal vars Global variables
printXML Print an XML representation of the object
Function : Print an XML representation of the object. Argument : A Genetics::StudyVariable object and the 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.
Function : Generate an HTML representation of the object. Argument : A Genetics::StudyVariable 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.
To install Genetics, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Genetics
CPAN shell
perl -MCPAN -e shell install Genetics
For more information on module installation, please visit the detailed CPAN module installation guide.