Masterarbeit, Heidi Lischer

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== PGD file example ======
Data of two loci with different data types (Standard and DNA) from two diploid populations:
<code>
<?xml version="1.0" encoding="iso-8859-1"?>
<?xml-stylesheet type="text/xsl" href="stylesheet_data-format3.xsl"?>

<PGD xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="PGD_schema.xsd">

  <header title="Fake HLA data">
    <numPop> 2 </numPop> 
    <ploidy> 1 </ploidy>  
    <missing> ? </missing>
    <gap> - </gap>
    <gameticPhase> known </gameticPhase>
  </header>


  <dataDescription>
    <numLoci> 2 </numLoci>
    <dataType> mixed </dataType>
    <locus id="loci one">
      <locusDataType> Standard </locusDataType>
      <locusChromosome> 3 </locusChromosome>
      <locusLocation> Hs8_23892 </locusLocation>
    </locus>
    <locus id="loci two">
      <locusDataType> DNA </locusDataType>
      <locusChromosome> 3 </locusChromosome>
      <locusLocation> Hs8_23992 </locusLocation>
      <locusLength> 29 </locusLength>
    </locus>   
  </dataDescription>
 

  <population name="A sample of 6 Algerians">
    <popSize> 7 </popSize> 
    <ind name="1">
      <indLoci> loci one </indLoci> 
      <data> 1104 </data>
    </ind>
    <ind name="2">
      <indLoci> loci one </indLoci> 
      <data> 0302 </data>
    </ind>
    <ind name="3">
      <indLoci> loci one </indLoci>     
      <data> 0402 </data>      
    </ind> 
    <ind name="1">
      <indLoci> loci two   </indLoci> 
      <data> GACTCTCTACGTAGCATCCGATGACGATA </data>
    </ind>
    <ind name="2">
      <indLoci> loci two </indLoci> 
      <data> GACTGTCTGCGTAGCATACGACGACGATA </data>
    </ind>
    <ind name="3">
      <indLoci> loci two </indLoci> 
      <data> GCCTGTCTGCGTAGCATAGGATGACGATA </data>
    </ind>
    <ind name="4">
      <indLoci> loci two </indLoci> 
      <data> GACTCTCTACGTAGCATCCGATGACGATA </data>
    </ind>
  </population>

  <population name="A sample of 11 Bulgarians">
    <popSize>4</popSize>
    <ind name="5">
      <indLoci> loci one </indLoci>
      <data> 1103</data>
    </ind>
    <ind name="6">
      <indLoci> loci one </indLoci>
      <data> 1101</data>
    </ind> 
    <ind name="5">
      <indLoci> loci two </indLoci> 
      <data> GCCTGTCTGCGTAGCATAGGATGACGATA </data>
    </ind>
    <ind name="6">
      <indLoci> loci two </indLoci> 
      <data> GACTCTCTACGTAGCATCCGATGACGATA </data>
    </ind>
  </population>


  <structure name="My population structure">
    <numGroups> 2 </numGroups>
    <group>A sample of 6 Algerians </group>
    <group>A sample of 11 Bulgarians </group>
  </structure>

  <distanceMatrix name="Faked distance matrix">
    <matrixSize> 6 </matrixSize>
    <matrixLabels> 1, 2, 3, 5, 6 </matrixLabels>
    <matrix> 0
             1, 0
             3, 4, 0
             5, 3, 2, 0
             6, 5, 4, 3, 0
    </matrix>
  </distanceMatrix>

</PGD>
</code>