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<p class="MsoNormal">Hi Thibaut, <o:p></o:p></p>
<p class="MsoNormal">I’m working on building a function that uses the seploc function on a tetraploid genind object that has a single microsatellite locus with two alleles (e.g. A and B). I’m a bit puzzled by the function’s behaviour....<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If I have a genind object called “example” and type:<o:p></o:p></p>
<p class="MsoNormal">>example@ploidy<o:p></o:p></p>
<p class="MsoNormal">The output is: <o:p></o:p></p>
<p class="MsoNormal">>4<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">However if I try:<o:p></o:p></p>
<p class="MsoNormal">>seploc(example)[[1]]@ ploidy<o:p></o:p></p>
<p class="MsoNormal">I get:<o:p></o:p></p>
<p class="MsoNormal">>2<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Why would the ploidy change if I separated the loci (just as a note in case it’s not obvious, this is just a test case)? I obtained the same result when I duplicated the locus and repeated these steps (checking to see if it might have been
due to running seploc on an individual with only one locus). I obtained a similar result when I tried seploc on genind objects with initial ploidies of 3 and 6. In the initial step I got ploidies = 3 or 6 and in the second step I got ploidy = 2.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for the help,<o:p></o:p></p>
<p class="MsoNormal">-Aaron<o:p></o:p></p>
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