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 examples ======
Data of two loci with Standard data type from four diploid populations: 
<code>
<?xml version="1.0" encoding="iso-8859-1"?>

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

  <header title="Fake HLA data">
    <numPop> 4 </numPop>
    <ploidy> 2 </ploidy>    
    <missing> ? </missing>
    <gap> - </gap>
    <gameticPhase> known </gameticPhase>
  </header>


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

  <population name="A sample of 6 Algerians">
    <popSize> 3 </popSize>
    <popLoci> loci one, loci two </popLoci>
    <ind name="1">
      <indGeogCoord> 35, 4 </indGeogCoord>
      <indLingGroup> African </indLingGroup>
      <data> 1104, 0200 </data>
      <data> 0700, 0301 </data>
    </ind>
    <ind name="3">
      <indGeogCoord> 36, 4 </indGeogCoord>
      <indLingGroup> Africanic </indLingGroup>
      <data> 0302, 0200 </data>
      <data> 1310, 0402 </data>
    </ind>
    <ind name="4">
      <indGeogCoord> 35, 5 </indGeogCoord>
      <indLingGroup> Africanical </indLingGroup>
      <data> 0402, 0602 </data>
      <data> 1502, 0602 </data>
    </ind>
  </population>

  <population name="A sample of 11 Bulgarians">
    <popSize>6</popSize>
    <popGeogCoord> 35, 4 </popGeogCoord>
    <popLingGroup> African </popLingGroup>
    <popLoci> loci one, loci two </popLoci>
    <ind name="1">
      <data> 1103, 0301 </data>
      <data> 0301, 0200 </data>
    </ind>
    <ind name="2">
      <data> 1101, 0301 </data>
      <data> 0700, 0200 </data>
    </ind>
    <ind name="3">
      <data> 1500, 0502 </data>
      <data> 0301, 0200 </data>
    </ind>
    <ind name="4">
      <data> 1103, 0301 </data>
      <data> 1202, 0301 </data>
    </ind>
    <ind name="5">
      <data> 0301, 0200 </data>
      <data> 1500, 0601 </data>
    </ind>
    <ind name="6">
      <data> 1600, 0502 </data>
      <data> 0301, 0603 </data>
    </ind>
  </population>

  <population name="A sample of 12 Egyptians">
    <popSize>6</popSize>
    <popLoci> loci one, loci two </popLoci>
    <ind name="1">
      <data> 1104, 0301 </data>
      <data> 1600, 0502 </data>
    </ind>
    <ind name="3">
      <data> 1303, 0301 </data>
      <data> 1101, 0502 </data>
    </ind>
    <ind name="4">
      <data> 1502, 0601 </data>
      <data> 1500, 0602 </data>
    </ind>
    <ind name="6">
      <data> 1101, 0301 </data>
      <data> 1101, 0301 </data>
    </ind>
    <ind name="8">
      <data> 1302, 0502 </data>
      <data> 1101, 0609 </data>
    </ind>
    <ind name="9">
      <data> 1500, 0302 </data>
      <data> 0402, 0602 </data>
    </ind>
  </population>

  <population name="A sample of 8 French">
    <popSize>4</popSize>
    <popLoci> loci one, loci two </popLoci>
    <ind name="219">
      <number_strains> 2 </number_strains>
      <data> 0301, 0200 </data>
      <data> 0101, 0501 </data>
    </ind>
    <ind name="239">
      <number_strains> 2 </number_strains>
      <data> 0301, 0200 </data>
      <data> 0301, 0200 </data>
    </ind>
    <ind name="249">
      <number_strains> 2 </number_strains>
      <data> 1302, 0604 </data>
      <data> 1500, 0602 </data>
    </ind>
    <ind name="250">
      <number_strains> 2 </number_strains>
      <data> 1401, 0503 </data>
      <data> 1301, 0603 </data>
    </ind>
  </population>

  <structure name="My population structure">
    <numGroups> 2 </numGroups>
    <group> A sample of 6 Algerians, A sample of 12 Egyptians </group>
    <group> A sample of 11 Bulgarians, A sample of 8 French </group>
  </structure>

  <distanceMatrix name="Faked distance matrix">
    <matrixSize> 11 </matrixSize>
    <matrixLabels> 1, 2, 3, 4, 6, 8, 9, 219, 239, 249, 250 </matrixLabels>
    <matrix> 0
             1, 0
             3, 4, 0
             5, 3, 2, 0
             6, 5, 3, 2, 0
             6, 7, 5, 3, 2, 0
             1, 2, 3, 5, 3, 2, 0
             4, 5, 6, 7, 5, 3, 2, 0
             1, 2, 3, 4, 5, 5, 3, 2, 0
             0, 9, 8, 7, 6, 5, 5, 3, 2, 0
             9, 8, 7, 6, 5, 4, 3, 5, 3, 2, 0
             5, 6, 7, 8, 9, 1, 2, 3, 5, 3, 2, 0
    </matrix>
  </distanceMatrix>

</PGD>
</code>