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<p class="MsoNormal">Dear all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">In my research I constantly work with genetic risk scores based on a large amount of SNPs. Sometimes it is appropriate to prune the SNPs by LD before constructing the genetic risk score to obtain a set of independent SNPs. The most widely
used function for this (plink --indep-pairwise) uses a sliding window to find pairs of SNPs in high LD with each other according to their R^2 and then removes one. However, it removes the SNP with the lowest minor allele frequency. In practice we may instead
want to keep the SNP with the lowest p-value: i.e. the most important to us. This should lead to higher quality genetic risk scores.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have written a function that reads in a list of SNPs and then prunes it for LD by choosing which SNP to remove from a pair in high LD according to its position in the snp list. So the SNP that comes first in the SNP list will never be
pruned out, and the second one only if it is in LD with the first one. The LD structure is based on your own data: it relies on the probabel configuration file for filepaths, and on databel for accessing the dosages.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I initially did this just to apply it to my own data, but Lennart suggested it might be a nice addition to genabel. I am interested in developing this further if there is indeed interest in such a function. If so I will share the code and
we can go from there.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Let me know what you think,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Paul<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL">P.S. de Vries<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL">PhD Scientist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL">Cardiovascular group<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL">Department of Epidemiology<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL">Erasmus MC, University Medical Center Rotterdam<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL">Office Ee 21-33<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL">PO Box 2040, 3000 CA Rotterdam,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL">The Netherlands<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL">Email:
<a href="mailto:p.s.devries@erasmusmc.nl"><span style="color:blue">p.s.devries@erasmusmc.nl</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New";color:#1F497D;mso-fareast-language:NL"><a href="http://www.erasmus-epidemiology.nl/"><span style="color:blue">http://www.erasmus-epidemiology.nl/</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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