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Hi there, <br>
<br>
as this question is also pegas-related, it may be better suited on
R-sig-genetics (I am not sure Emmanuel Paradis reads the adegenet
forum): <br>
<a class="moz-txt-link-freetext" href="https://stat.ethz.ch/mailman/listinfo/r-sig-genetics">https://stat.ethz.ch/mailman/listinfo/r-sig-genetics</a><br>
<br>
This list was typically a bit of a deadland but we are trying to
resurrect it.<br>
<br>
Cheers<br>
Thibaut<br>
<br>
<div class="moz-cite-prefix">On 06/04/15 14:48, Virgilio
Massimiliano wrote:<br>
</div>
<blockquote
cite="mid:702BA0C8-1B27-4C0E-8E1C-41E36FADFB65@africamuseum.be"
type="cite">
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<div class="" style="word-wrap:break-word">hi,
<div class="">I’m trying to make a bootstrapped njt on msat
data,</div>
<div class="">as far as I can understand, it’s not possible to
bootstrap my loci starting from a genind object and this:</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">myBoots <- boot.phylo(NJtree,
data_genind@tab, B =100, function(xx) njs(dist(xx)))</div>
<div class=""><br class="">
</div>
<div class="">shouldn’t be correct as it bootstraps alleles
(data_genind@tab)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">So I’m trying to convert my genind data into
loci using genind2loci and read.loci :</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
<div class="">
<div class="">library(adegenet)</div>
<div class="">data <- read.genetix("data.gtx")</div>
<div class="">
<div class="">data_loci<-genind2loci(data)</div>
<div class="">write.csv(data_loci, file = "data_loci.csv")</div>
<div class="">library(pegas)</div>
<div class="">data_pegas<-read.loci(file =
"data_loci.csv", loci.sep = ",")</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">and then get the tree (based on Fst, but it
doesn’t work either with distances)</div>
<div class=""><br class="">
</div>
<div class="">pairFst <- pairwise.fst(data,
res.type="matrix", truenames=TRUE)</div>
<div class=""><br class="">
</div>
</div>
</div>
<div class="">
<div class="">library(ape)</div>
<div class="">njtreFst_pop <- njs(pairFst)</div>
<div class="">
<div class="">myBoots <- boot.phylo(njtreFst_pop,
as.matrix(data_pegas), B = 3, function(xx)</div>
<div class=""> njs(dist(xx)))</div>
<div class=""><br class="">
</div>
</div>
</div>
<div class="">but it doesn’t seem to work (I’m attaching the
input file) and I get only error messages no matter what I
try...</div>
</div>
<div class=""><br class="">
</div>
<div class="">What am I doing wrong? Is there a simpler way of
getting bootstrapped msat loci starting form a genind object?</div>
<div class=""><br class="">
</div>
<div class="">greeting and many thanks in advance</div>
<div class=""><br class="">
</div>
<div class="">Massi</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
<div class="" style="word-wrap:break-word">
<div class=""><br class="">
<div class="">
<div class="" style="color:rgb(0,0,0);
letter-spacing:normal; orphans:auto; text-align:start;
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style="border-collapse:separate; border-spacing:0px">
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class="x_Apple-style-span"
style="border-collapse:separate; orphans:2;
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class="x_Apple-style-span"
style="border-collapse:separate; orphans:2;
text-indent:0px; widows:2; border-spacing:0px">
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class="x_Apple-style-span"
style="border-collapse:separate; orphans:2;
text-indent:0px; widows:2;
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style="border-collapse:separate;
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style="word-wrap:break-word"><span
class="x_Apple-style-span"
style="border-collapse:separate;
orphans:2; text-indent:0px;
widows:2;
border-spacing:0px">
<div class=""
style="color:rgb(0,0,0);
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__________________________________</div>
<div class=""
style="color:rgb(0,0,0);
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<font
class="x_Apple-style-span"
color="#004D95"> Massimiliano
Virgilio, PhD <br
class="">
<br class="">
Royal Museum for Central
Africa <br class="">
<br class="">
</font></div>
<div class=""
style="word-wrap:break-word"><font
class="x_Apple-style-span" color="#004D95">Joint Experimental Molecular Unit
(JEMU)</font></div>
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<font
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class="">
</font></div>
<div class=""
style="color:rgb(0,0,0);
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<font
class="x_Apple-style-span"
color="#004D95">Leuvensesteenweg
13, B-3080
Tervuren, Belgium, +32
(0) 27695366<br class="">
<br class="">
<a
moz-do-not-send="true"
href="mailto:massimiliano.virgilio@africamuseum.be" class="">massimiliano.virgilio@africamuseum.be</a> <br
class="">
<br class="">
<a
moz-do-not-send="true"
href="http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/"
class="">http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/</a></font></div>
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<font
class="x_Apple-style-span"
color="#004D95"><br
class="">
</font></div>
<div class=""
style="word-wrap:break-word"><font
class="x_Apple-style-span" color="#004D95"><a moz-do-not-send="true"
href="http://jemu.myspecies.info"
class="">http://jemu.myspecies.info</a></font></div>
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<font
class="x_Apple-style-span"
color="#2900D2"><br
class="">
</font></div>
</span></div>
</span></div>
</span></span></span></span></span></div>
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</div>
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