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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hello,
<br>
<br>
normally the results should be the same, although clusters found by find.clusters will likely differ from one run to another. E.g. cluster 1 will become 4 etc.
<br>
<br>
Are you sure this is not the source of the differences? If you want to check that the data are identical, you can compare the matrices of individual frequencies:<br>
all.equal(x1$tab,x2$tab)<br>
<br>
where x1 and x2 are genind imported with different methods.<br>
<br>
I would need at least a head(tab) to check that df2genind is well used.<br>
<br>
Cheers<br>
<br>
Thibaut<br>
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<div style="direction: ltr;" id="divRpF932307"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Huang,Cheng-Hua [arhua@ufl.edu]<br>
<b>Sent:</b> 04 July 2011 16:09<br>
<b>To:</b> Jombart, Thibaut; adegenet-forum@r-forge.wu-wien.ac.at<br>
<b>Cc:</b> arhuahuang@gmail.com<br>
<b>Subject:</b> RE: [adegenet-forum] Structure-like membership plot<br>
</font><br>
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<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Arial","sans-serif"; color: black;">Dear Thibaut,</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Arial","sans-serif"; color: black;"> </span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Arial","sans-serif"; color: black;">Thank you for your help. I used the way you advised me to convert the Strucutre file of my haploid data
set into a genind object as follow: </span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Arial","sans-serif"; color: black;"> </span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Arial","sans-serif"; color: black;">dat <- read.table("structure.str", sep="\t",head=TRUE)</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">x <- df2genind(dat[,-(1:2)], ploidy=1, pop=dat[,2], ind.names=dat[,1])</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;"></span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">and then<br>
<br>
###<br>
find.cluster(x)<br>
dapc(x)</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">…</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;"><br>
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">However,
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">the membership plot derived from th</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">is Structure
file</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">(showing admixture individuals)
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">was different
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">those obtained from using
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif";">import2genind
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif";">to convert
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">Genepop and Fstat files
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">of the same data set where data were coded as
</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">a pseudo-diploid</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;"> (no admixture individuals).
Did I convert my structure data set wrong? Or, I should trust results from </span>
<span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">Genepop and Fstat</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;"> data sets? Thank you.</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">Regards,
</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif"; color: black;">Arhau</span><span style="font-size: 12pt; line-height: 115%; font-family: "Arial","sans-serif";"></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span></p>
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<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><b><span style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Jombart, Thibaut [mailto:t.jombart@imperial.ac.uk]
<br>
<b>Sent:</b> Monday, July 04, 2011 9:30 AM<br>
<b>To:</b> Huang,Cheng-Hua; adegenet-forum@r-forge.wu-wien.ac.at<br>
<b>Cc:</b> arhuahuang@gmail.com<br>
<b>Subject:</b> RE: [adegenet-forum] Structure-like membership plot</span></p>
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<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: black;">Dear Arhua,
<br>
<br>
read.structure is only meant for diploid data - will add a warning on this point in the doc for 1.3-1.
<br>
<br>
So your analysis based on read.structure here is wrong. The other analyses are surely OK. Otherwise use read.table/read.csv to read your structure data into R as a data.frame, and then df2genind with the proper arguments to convert the data into a genind object.<br>
<br>
Best<br>
<br>
Thibaut</span></p>
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<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: black;">--
<br>
######################################<br>
Dr Thibaut JOMBART<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - Faculty of Medicine<br>
St Mary’s Campus<br>
Norfolk Place<br>
London W2 1PG<br>
United Kingdom<br>
Tel. : 0044 (0)20 7594 3658<br>
t.jombart@imperial.ac.uk<br>
http://sites.google.com/site/thibautjombart/<br>
http://adegenet.r-forge.r-project.org/</span></p>
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<p class="MsoNormal" style="margin-bottom: 12pt; line-height: normal;"><b><span style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: black;">From:</span></b><span style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: black;"> adegenet-forum-bounces@r-forge.wu-wien.ac.at
[adegenet-forum-bounces@r-forge.wu-wien.ac.at] on behalf of Cheng-Hua Huang [arhua@ufl.edu]<br>
<b>Sent:</b> 01 July 2011 17:10<br>
<b>To:</b> adegenet-forum@r-forge.wu-wien.ac.at<br>
<b>Cc:</b> arhuahuang@gmail.com<br>
<b>Subject:</b> [adegenet-forum] Structure-like membership plot</span><span style="font-size: 12pt; font-family: "Times New Roman","serif"; color: black;"></span></p>
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<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; color: black;">Dear adegent users and Thibaut,</span><span style="color: black;"></span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; color: black;">I would like to ask questions about using DAPC. I have used
</span><span style="color: black;">import2genind</span><span style="font-size: 12pt; line-height: 115%; color: black;"> and
</span><span style="font-size: 10pt; line-height: 115%; font-family: "Tahoma","sans-serif"; color: black;">df2genind</span><span style="font-size: 12pt; line-height: 115%; color: black;"> for importing Structure, Genepop, and Fstat files of the same data set
to find clusters and to plot Struture-like membership information. Since I was working on a haploid, asexual fungus collected from three regions, I coded data sets as a pseudo-diploid for Genepop and Fstat files but used the original haploid data set for the
Structure format. Even though I got K=3 for biological interpretation based on BIC, the membership plot derived from the Structure input file was different from those obtained from the other two file formats. The result using the Structure input format showed
many admixture individuals, but the other two input files did not exhibit any admixture individuals (all with membership probability = 1). The latter makes sense to me because the fungus is asexual and genotype flow plays a main role in shaping population
structure. Moreover, recombination is not possible for this fungus. Thus, admixture individuals may not occur. What caused this difference between these input files? How do I interpret these results? Thank you for your help.</span><span style="color: black;"></span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; color: black;">Regards,</span><span style="color: black;"></span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; color: black;">Arhua</span><span style="color: black;"></span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; color: black;"> </span><span style="color: black;"></span></p>
<p class="MsoNormal"><span style="color: black;"> </span></p>
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