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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hello adegenet-forum-members,<br>
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I wanted to use your R package adegenet to convert a dataframe into genind-class. My dataframe contains ~9800 samples (in rows) and ~87600 markers (in columns). Genotypes are coded like "AG", "TT", and so on.<br>
Example (5x5 extract):<br>
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<table cellpadding="0" cellspacing="0" width="480" border="0" style="border-collapse:collapse; width:360pt">
<colgroup><col span="6" width="80" style="width:60pt"></colgroup>
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<tr height="20" style="height:15.0pt">
<td height="20" width="80" style="height:15.0pt; width:60pt"><br>
</td>
<td width="80" style="width:60pt">marker1</td>
<td width="80" style="width:60pt">marker2</td>
<td width="80" style="width:60pt">marker3</td>
<td width="80" style="width:60pt">marker4</td>
<td width="80" style="width:60pt">marker4</td>
</tr>
<tr height="20" style="height:15.0pt">
<td height="20" style="height:15.0pt">Samp1</td>
<td>GA</td>
<td>GA</td>
<td>AA</td>
<td>TT</td>
<td>TT</td>
</tr>
<tr height="20" style="height:15.0pt">
<td height="20" style="height:15.0pt">Samp2</td>
<td>AA</td>
<td>AA</td>
<td>CA</td>
<td>CT</td>
<td>TT</td>
</tr>
<tr height="20" style="height:15.0pt">
<td height="20" style="height:15.0pt">Samp3</td>
<td>GA</td>
<td>GA</td>
<td>CA</td>
<td>TT</td>
<td>TT</td>
</tr>
<tr height="20" style="height:15.0pt">
<td height="20" style="height:15.0pt">Samp5</td>
<td>GA</td>
<td>AA</td>
<td>CA</td>
<td>TT</td>
<td>TT</td>
</tr>
<tr height="20" style="height:15.0pt">
<td height="20" style="height:15.0pt">Samp6</td>
<td>AA</td>
<td>AA</td>
<td>AA</td>
<td>TT</td>
<td>TT</td>
</tr>
</tbody>
</table>
<br>
I have been tryingt to run the df2genind for days now (df2genind(dataframe, ploidy=as.integer(2))), but it's not finishing or maybe not working. The question is now, can your function handle such big dataframes like this or could there be another problem? (It's
running on a quit good server, so it shouldn't be due too little sever capacity/memory.)<br>
<br>
I also tried to convert parts of the dataframe (always 5000 marker, all ~9800 individuals) to genind and use afterwords your repool-command. But here we have the problem, that the genind-classes don't have the same length in the end.<br>
<br>
I could also use PED/MAP- or .raw-files from PLINK as input, but in the end I need a genind-object!<br>
<br>
Do you have any idea how to solve this problem? <br>
<br>
Best Regards,<br>
Julia Bischof<br>
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