<div dir="ltr"><div>Hi Zhian</div><div><br></div><div>I use the following (one example with my U2166dapc.csv file)</div><div>my data are haploid, with headers, 1colum for individual ID, 10 next columns with microsatellite data</div><div>
<p class="gmail-MsoNormalCxSpFirst" style="line-height:normal"><br></p><p class="gmail-MsoNormalCxSpFirst" style="line-height:normal">U2166 <-
read.csv2(file = "U2166dapc.csv", header = TRUE, sep = ",")</p><p class="gmail-MsoNormalCxSpFirst" style="line-height:normal"><br></p><p class="gmail-MsoNormalCxSpFirst" style="line-height:normal">then ,</p><p class="gmail-MsoNormalCxSpFirst" style="line-height:normal"><br></p><p class="gmail-MsoNormalCxSpFirst" style="line-height:normal">
</p><p class="gmail-MsoNormalCxSpFirst" style="line-height:normal">U2166genind <-
df2genind(U2166[,c(2:12)], sep = ",", ploidy = 1)<span></span></p>
</div><div><br></div><div>and then I find clusters on the genind object</div><div><br></div><div>hope it helps...</div><div>eugenia</div><div><br></div><div><p class="gmail-MsoNormalCxSpFirst" style="line-height:normal"><br></p><p class="gmail-MsoNormalCxSpFirst" style="line-height:normal"><br></p><p class="gmail-MsoNormalCxSpFirst" style="line-height:normal"><span></span></p>
</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Feb 2, 2020 at 9:02 PM Zhian Kamvar <<a href="mailto:kamvarz@science.oregonstate.edu">kamvarz@science.oregonstate.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hello,</div><div><br></div><div>You can import your data with read.csv() and then use `as.genlight()` to convert the allele counts into a genlight object.<br></div><div>Hope that helps.</div><div><br></div><div>Best, Zhian<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Feb 1, 2020 at 11:00 AM <<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org" target="_blank">adegenet-forum-request@lists.r-forge.r-project.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send adegenet-forum mailing list submissions to<br>
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1. potato dosage SNP (weiya xue)<br>
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Message: 1<br>
Date: Fri, 31 Jan 2020 12:04:18 -0500<br>
From: weiya xue <<a href="mailto:xueweiya@gmail.com" target="_blank">xueweiya@gmail.com</a>><br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: [adegenet-forum] potato dosage SNP<br>
Message-ID:<br>
<<a href="mailto:CAK59EjBEo0sko7MY2AQvH%2BL%2BUOrTRAxxpMuDU_twsGbLvOz1Zg@mail.gmail.com" target="_blank">CAK59EjBEo0sko7MY2AQvH+L+UOrTRAxxpMuDU_twsGbLvOz1Zg@mail.gmail.com</a>><br>
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<br>
Dear Dr. Zhian N. Kamvar,<br>
<br>
I am potato postdoc researcher at Pennsylvania state university. I<br>
have a question when I use adegenet R package for DAPC analysis .<br>
<br>
My SNP data were coded as dosage 0,1,2,3,4 in csv file(sample data<br>
attached). When I used read.csv to read this data into R, which<br>
function should I use to convert it into adegent format for next<br>
steps?<br>
<br>
<br>
<br>
And when I use read.structure, I always get the below information.<br>
<br>
<br>
<br>
Error in mat[, (ncol(mat) - p + 1):ncol(mat)] :<br>
<br>
only 0's may be mixed with negative subscripts<br>
<br>
<br>
<br>
Thanks a lot,<br>
<br>
Weiya Xue<br>
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