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Just to add my two cents,
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<div>there is also <span style="background-color:rgb(255,255,255)"><font face="Times">read.plink {snpMatrix} which returns a simple matrix, might require less from the RAM point of view.</font></span></div>
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<div><span style="background-color:rgb(255,255,255)"><font face="Times">Nicola</font></span></div>
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<div>Dr. Nicola Pirastu PhD<br>
Research Fellow<br>
Medical Sciences, Chirurgical and Health Department<br>
University of Trieste<br>
Medical Genetics <br>
IRCCS Burlo Garofolo<br>
Via dell'Istria 65/1<br>
34137 Italy<br>
tel. +390403785539 </div>
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<div>Il giorno 22/nov/2013, alle ore 11:23, Maarten Kooyman <<a href="mailto:m.kooijman@erasmusmc.nl">m.kooijman@erasmusmc.nl</a>> ha scritto:</div>
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snpStats does have a GPL-3 licence, so we can use the code and do whatever we want with it so long as we keep it under the same licence and give credit to to the owner/writer of the code.<br>
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Is it possible to adjust the snpStats code to dump the genotypes of the bed file directly into DatABEL format? This sound to me as the fastest(as in CPU time) option.<br>
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Maarten Kooyman<br>
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On 11/22/2013 11:08 AM, L.C. Karssen wrote:<br>
<span style="white-space:pre">> Thanks Maarten, that's a good finding. It does seem to return the data<br>
> (incl. genotype data) in a list. I'm not sure how well that will work<br>
> RAM-wise for large data sets. On the other hand the function does allow<br>
> SNP selection, so maybe conversion could be done per chromosome.<br>
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