Genetics
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<th width="99%" colspan="3" align="Left"><font face="Courier New, Courier, mono" color="#000080" size="5">Required Attributes</font></th>
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<th width="14%">Name</th>
<th width="45%">Data type and Format</th>
<th width="40%">Description</th>
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<td width="14%"> <font face="Courier New, Courier, mono" color="#000080" > category </font></td>
<td width="45%"> String ("Trait", "StaticAffectionStatus", "StaticLiabilityClass", "DynamicAffectionStatus", "Environment", or "Treatment") </td>
<td width="40%"> Default value = "Trait" <br> DynamicAffectionStatus variables are not yet implemented.</td>
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<td width="14%"> <font face="Courier New, Courier, mono" color="#000080" > format </font></td>
<td width="45%"> String ("Number", "Code", "Date", "DerivedNumber", or "DerivedCode") </td>
<td width="40%"> The value of format determines the datatype of the Phenotype values associated with the StudyVariable. </td>
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<td width="14%"> <font face="Courier New, Courier, mono" color="#000080" > isXLinked </font></td>
<td width="45%"> Boolean (1 or 0) </td>
<td width="40%"> Default value = 0 </td>
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<tr bgcolor="#d9d5d5">
<th width="99%" colspan="3" align="Left"><font face="Courier New, Courier, mono" color="maroon" size="5">Optional Attributes</font></th>
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<th width="14%">Name</th>
<th width="45%">Data type and Format</th>
<th width="40%">Description</th>
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<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > description </font></td>
<td width="45%"> String (<= 255 characters) </td>
<td width="40%"> </td>
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<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > lowerBound </font></td>
<td width="45%"> Float (12,5) OR String ("YYYY-MM-DD") </td>
<td width="40%"> Only appropriate for StudyVariables with a format of Number or Date. </td>
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<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > upperBound </font></td>
<td width="45%"> Float (12,5) OR String ("YYYY-MM-DD") </td>
<td width="40%"> Only appropriate for StudyVariables with a format of Number or Date. </td>
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<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > Codes </font></td>
<td width="45%"> Array pointer to a list of hash pointers. The referenced hashes should have the following key/value structure: <br>
<font face="Courier New, Courier, mono" color="#000080" > code </font> => Integer (<= 99) <br>
<font face="Courier New, Courier, mono" color="maroon" > description </font> => String (<= 255 characters) <br>
<font face="Courier New, Courier, mono" color="maroon" > formula </font> => String (<= 65535 characters) </td>
<td width="40%"> Only appropriate for StudyVariables with a format of Code or DerivedCode. A formula is required for each Code definition if the format is DerivedCode</td>
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<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > AffStatDef </font></td>
<td width="45%"> Hash pointer. The referenced hash should have the following key/value structure: <br>
<font face="Courier New, Courier, mono" color="#000080" > name </font> => String (<= 120 characters) <br>
<font face="Courier New, Courier, mono" color="#000080" > diseaseAlleleFreq </font> => Float (7,6) <br>
<font face="Courier New, Courier, mono" color="#000080" > pen11 </font> => Float (7,6) <br>
<font face="Courier New, Courier, mono" color="#000080" > pen12 </font> => Float (7,6) <br>
<font face="Courier New, Courier, mono" color="#000080" > pen22 </font> => Float (7,6) <br>
<font face="Courier New, Courier, mono" color="maroon" > AffStatElements </font> => Array reference to a list of anonymous hashes (see Example).</td>
<td width="40%"> Only appropriate for StudyVariables with a format of DynamicAffectionStatus. DynamicAffectionStatus variables are not yet implemented; the data in this field is stored in the database, but it is not used for anything. <p> When Dyn...
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<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > LCDef </font></td>
<td width="45%"> Hash pointer. The referenced hash should have the following key/value structure: <br>
<font face="Courier New, Courier, mono" color="#000080" > name </font> => String (<= 120 characters) <br>
<font face="Courier New, Courier, mono" color="maroon" > LiabilityClasses </font> => Array reference to a list of anonymous hashes (see Example).</td>
<td width="40%"> Only appropriate for StudyVariables with a category of DynamicAffectionStatus. DynamicAffectionStatus variables are not yet implemented; the data in this field is stored in the database, but it is not used for anything. <p> When D...
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<p>
<b>Example:</b>
<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>
<HR>
<H2><a name="subject"></a>Genetics::Object::Subject</H2>
<table border="0" width="99%" cellspacing="1" cellpadding="2">
<tr bgcolor="#d9d5d5">
<th width="99%" colspan="3" align="Left"><font face="Courier New, Courier, mono" color="#000080" size="5">Required Attributes</font></th>
</tr>
<tr bgcolor="#d9d5d5">
<th width="14%">Name</th>
<th width="45%">Data type and Format</th>
<th width="40%">Description</th>
</tr>
<tr bgcolor="#d9d5d5">
<td width="14%"> <font face="Courier New, Courier, mono" color="#000080" > gender </font></td>
<td width="45%"> String ("Unknown", "Male", "Female", or "Both") </td>
<td width="40%"> </td>
</tr>
<tr bgcolor="#d9d5d5">
<th width="99%" colspan="3" align="Left"><font face="Courier New, Courier, mono" color="maroon" size="5">Optional Attributes</font></th>
</tr>
<tr bgcolor="#d9d5d5">
<th width="14%">Name</th>
<th width="45%">Data type and Format</th>
<th width="40%">Description</th>
</tr>
<tr bgcolor="#d9d5d5">
<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > dateOfBirth </font></td>
<td width="45%"> String ("YYYY-MM-DD") </td>
<td width="40%"> </td>
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<tr bgcolor="#d9d5d5">
<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > dateOfDeath </font></td>
<td width="45%"> String ("YYYY-MM-DD") </td>
<td width="40%"> </td>
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<tr bgcolor="#d9d5d5">
<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > isProband </font></td>
<td width="45%"> Boolean (1 or 0) </td>
<td width="40%"> Default value = 0. </td>
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<tr bgcolor="#d9d5d5">
<td width="14%"> <font face="Courier New, Courier, mono" color="maroon" > Mother </font></td>
<td width="45%"> <a href="#refs">Subject Reference</a></td>
<td width="40%"> </td>
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