Genetics
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<LI><A HREF="#name">NAME</A></LI>
<LI><A HREF="#synopsis">SYNOPSIS</A></LI>
<LI><A HREF="#description">DESCRIPTION</A></LI>
<LI><A HREF="#license">LICENSE</A></LI>
<LI><A HREF="#feedback">FEEDBACK</A></LI>
<LI><A HREF="#author steve mathias">AUTHOR - Steve Mathias</A></LI>
<LI><A HREF="#details">DETAILS</A></LI>
<LI><A HREF="#imported packages">Imported Packages</A></LI>
<LI><A HREF="#public methods">Public methods</A></LI>
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<LI><A HREF="#printxml">printXML</A></LI>
<LI><A HREF="#ashtml">asHTML</A></LI>
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<P>
<H1><A NAME="name">NAME</A></H1>
<P>Genetics::StudyVariable</P>
<P>
<HR>
<H1><A NAME="synopsis">SYNOPSIS</A></H1>
<PRE>
$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"},
],
},
) ;
</PRE>
<PRE>
See the GenPerl Tutorial for more information.</PRE>
<P>
<HR>
<H1><A NAME="description">DESCRIPTION</A></H1>
<P>StudyVariable objects represent definitions of physical traits, affection
status loci, environmental exposure, or drug treatments.</P>
<P>
<HR>
<H1><A NAME="license">LICENSE</A></H1>
<P>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.</P>
<P>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.</P>
<P>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</P>
<P>
<HR>
<H1><A NAME="feedback">FEEDBACK</A></H1>
<P>Currently, all feedback should be sent directly to the author.</P>
<P>
<HR>
<H1><A NAME="author steve mathias">AUTHOR - Steve Mathias</A></H1>
<P>Email: <A HREF="mailto:mathias@genomica.com">mathias@genomica.com</A></P>
<P>Phone: (720) 565-4029</P>
<P>Address: Genomica Corporation
1745 38th Street
Boulder, CO 80301</P>
<P>
<HR>
<H1><A NAME="details">DETAILS</A></H1>
<P>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 (_).</P>
<P>
<HR>
<H1><A NAME="imported packages">Imported Packages</A></H1>
<PRE>
Genetics::Object Superclass
strict Just to be anal
vars Global variables</PRE>
<P>
<HR>
<H1><A NAME="public methods">Public methods</A></H1>
<PRE>
printXML Print an XML representation of the object</PRE>
<P>
<H2><A NAME="printxml">printXML</A></H2>
<PRE>
Function : Print an XML representation of the object.
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