<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:"Lucida Console";
panose-1:2 11 6 9 4 5 4 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal">For snapclust, it appears that it only reads genind objects and not genlight objects. This wasn’t mentioned in the tutorial, but I see this specified in the adegenet manual:<o:p></o:p></p>
<p class="MsoNormal">Usage snapclust(x, k, pop.ini = "ward", max.iter = 100, n.start = 10, n.start.kmeans = 50, hybrids = FALSE, dim.ini = 100, hybrid.coef = NULL, parent.lab = c("A", "B"), ...)
<o:p></o:p></p>
<p class="MsoNormal">Arguments <o:p></o:p></p>
<p class="MsoNormal"><span style="background:yellow;mso-highlight:yellow">x a genind object</span><o:p></o:p></p>
<p class="MsoNormal"><a href="https://cran.r-project.org/web/packages/adegenet/adegenet.pdf">https://cran.r-project.org/web/packages/adegenet/adegenet.pdf</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Given that genlight and snapclust (I think) were both developed primarily for large snp datasets, that doesn’t make sense to me. I assumed snapclust would use genlight objects, and it took me a while to realize otherwise. It might help
others to clarify.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal">Russell<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="line-height:9.0pt"><span style="font-size:9.0pt;font-family:"Lucida Console""><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><o:p> </o:p></p>
<p class="MsoNormal" style="background:white">Russell S. Pfau, PhD<o:p></o:p></p>
<p class="MsoNormal" style="background:white">Professor, Department of Biological Sciences<o:p></o:p></p>
<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
<p class="MsoNormal" style="background:white">Biological Sciences Box T-0100<o:p></o:p></p>
<p class="MsoNormal" style="background:white">Tarleton State University<o:p></o:p></p>
<p class="MsoNormal" style="background:white">Stephenville TX 76402<o:p></o:p></p>
<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
<p class="MsoNormal" style="background:white">254-968-9761<o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:#1F497D"><a href="http://faculty.tarleton.edu/pfau/" target="_blank"><span style="color:blue">http://faculty.tarleton.edu/pfau/</span></a></span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</body>
</html>