<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><html><head><meta content="text/html;charset=UTF-8" http-equiv="Content-Type"></head><body ><div style="font-family: Verdana, Arial, Helvetica, sans-serif; font-size: 10pt;"><div>When centering is turned on (default), there is some imputing happening. See code here:<br></div><div><br></div><div><a target="_blank" href="https://github.com/thibautjombart/adegenet/blob/9f24e97759c13e0edb1c700ca1e406d8dffcb1fd/R/glFunctions.R#L327">https://github.com/thibautjombart/adegenet/blob/9f24e97759c13e0edb1c700ca1e406d8dffcb1fd/R/glFunctions.R#L327</a><br></div><div><a target="_blank" href="https://github.com/thibautjombart/adegenet/blob/9f24e97759c13e0edb1c700ca1e406d8dffcb1fd/R/glFunctions.R#L351">https://github.com/thibautjombart/adegenet/blob/9f24e97759c13e0edb1c700ca1e406d8dffcb1fd/R/glFunctions.R#L351</a><br></div><div><br></div><div>HTH,<br></div><div>Roman</div><div><br></div><div id="Zm-_Id_-Sgn" data-sigid="1142245000000006003" data-zbluepencil-ignore="true"><div><br></div><div><div>--- <br></div><div>“If we have data, let’s look at data. If all we have are opinions, let’s go with mine.” -- Jim Barksdale<br></div></div><div><br></div></div><div><br></div><div class="zmail_extra_hr" style="border-top: 1px solid rgb(204, 204, 204); height: 0px; margin-top: 10px; margin-bottom: 10px; line-height: 0px; display: none;"><br></div><div class="zmail_extra" data-zbluepencil-ignore="true" style="clear: both;"><div><br></div><div id="Zm-_Id_-Sgn1">---- On Tue, 18 Feb 2025 17:19:57 +0100 <b>Taylor Naaykens <taylor.naaykens@utoronto.ca></b> wrote ---<br></div><div><br></div><blockquote style="margin: 0px;" id="blockquote_zmail"><div class="zm_911743194229134067_parse_1438074079764772605" style=""><div class="x_1246883542WordSection1"><p class="" style="margin-top: 0px; margin-bottom: 0px;">Hi,<br></p><p class="" style="margin-top: 0px; margin-bottom: 0px;"> <br></p><p class="" style="margin-top: 0px; margin-bottom: 0px;">I have search for the answer in the documentation and the forums and have come across this question a few times but never the answer. When running glPCA, how does this function handle missing data? Does it do a pairwise deletion for each
locus where there is missing data for that individual? Or does it automatically do mean imputation? I can’t find a concrete answer one way or the other in the forums.<br></p><p class="" style="margin-top: 0px; margin-bottom: 0px;"> <br></p><p class="" style="margin-top: 0px; margin-bottom: 0px;">Thanks<br></p><p class="" style="margin-top: 0px; margin-bottom: 0px;"> <br></p><p class="" style="margin-top: 0px; margin-bottom: 0px;"> <br></p><p class="" style="margin-top: 0px; margin-bottom: 0px;">Taylor<br></p></div></div>_______________________________________________<br>adegenet-forum mailing list <br>adegenet-forum@lists.r-forge.r-project.org <br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum <br></blockquote></div><div><br></div></div><br></body></html>