<div dir="ltr">Hi,<div><br></div><div> This worked. I could not figure out how to access $Hobs for each population without using a for loop.</div><div><br></div><div><div>x.pop = seppop(x)</div><div>summary.by.pop = lapply(x.pop, summary)</div><div>Hobs.ls = rep(NA, length(summary.by.pop))</div><div>for (i in 1:length(summary.by.pop)){</div><div> Hobs.ls[i] = mean(summary.by.pop[[i]]$Hobs)</div><div>}</div><div>barplot(Hobs.ls, names.arg = levels(pop(x)), las = 2, main = "Observed heterozygosity", ylab = "Ho")</div></div><div><br></div><div>Thank you very much for your help,</div><div><br></div><div>Simon</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Nov 23, 2015 at 10:38 AM, Jombart, Thibaut <span dir="ltr"><<a href="mailto:t.jombart@imperial.ac.uk" target="_blank">t.jombart@imperial.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">You can use 'seppop' to split your data by population, and then lapply over it to get population specific summaries (averaging over loci if you need).<br>
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Makes sense?<br>
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Cheers<br>
Thibaut<br>
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<div style="direction:ltr"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Simon Nadeau [<a href="mailto:simon.nadeau.ubc@gmail.com" target="_blank">simon.nadeau.ubc@gmail.com</a>]<br>
<b>Sent:</b> 23 November 2015 18:19<br>
<b>To:</b> Maria Guerrina<br>
<b>Cc:</b> Jombart, Thibaut; <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> Re: [adegenet-forum] How to get observed heterozygosity per population<br>
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<div dir="ltr">Hi Thibault,
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<div> Thank you very much for your help. I just downloaded the dev version but I get the same results using summary(x) than with the previous version. summary gives me expected and observed heterozygosity but per loci:</div>
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<div>summary(x)$Hobs</div>
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<div> What I would like to have is Hobs <u>per population</u> instead. Something similar to the function Hs but for Hobs. Is there anything like that in adegenet? I tried basic.stats from Hierfstat as Maria suggested, but I got an error message, probably
due to something wrong in the way I formatted the data.</div>
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<div>Simon</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Nov 23, 2015 at 6:58 AM, Maria Guerrina <span dir="ltr">
<<a href="mailto:maria.guerrina@edu.unige.it" target="_blank">maria.guerrina@edu.unige.it</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Thibaut!
<div>I have a problem similar to Simon.</div>
<div>I have tried to use the function 'summary', but I get 0 both for the observed heterozigosity both for the expected one...</div>
<div>I have tried to use the function 'basic.stats' in hierfstat, but it doesn't give a result for Ho, in my case with my data.</div>
<div><br>
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<div>any idea?</div>
<div>Thanks!</div>
<div>Maria<br>
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<div>Maria Guerrina PhD</div>
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<div>Università di Genova</div>
<div>DISTAV</div>
<div>Corso Dogali 1M</div>
<div>I - 16136 GENOVA (Italy)</div>
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<div><a href="mailto:maria.guerrina@edu.unige.it" target="_blank">maria.guerrina@edu.unige.it</a></div>
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<div>On 23/nov/2015, at 13.11, Jombart, Thibaut wrote:</div>
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Hello,<span> </span><br>
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have you tried 'summary'? Note, the current devel version is better (previous summary was returning invisibly a list).<span> </span><br>
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Cheers<br>
Thibaut<br>
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<div style="direction:ltr"><font color="#000000" face="Tahoma" size="2"><b>From:</b><span> </span><a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org" target="_blank">adegenet-forum-bounces@lists.r-forge.r-project.org</a><span> </span>[<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org" target="_blank">adegenet-forum-bounces@lists.r-forge.r-project.org</a>]
on behalf of Simon Nadeau [<a href="mailto:simon.nadeau.ubc@gmail.com" target="_blank">simon.nadeau.ubc@gmail.com</a>]<br>
<b>Sent:</b><span> </span>19 November 2015 23:00<br>
<b>To:</b><span> </span><a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Subject:</b><span> </span>[adegenet-forum] How to get observed heterozygosity per population<br>
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<div dir="ltr">Hi,
<div><br>
</div>
<div> I have recently been using the various features of adegenet unsing genind objects and I works great so far. However, I can't seem to be able to find easy summary stats:</div>
<div><br>
</div>
<div>Observed heterozygosity per population: this would be very handy but I only found the function Hs (expected heterozygosity).</div>
<div><br>
</div>
<div>Global allele frequencies per loci: there is a nice histogram of minor allele frequencies on page 30 of the adegenet genomic tutorial, but I can't find how to generate the same plot using genind objects.</div>
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<div>Thank you very much for your help,</div>
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<div>Simon<br clear="all">
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<div><font color="#3d85c6" size="4">Simon Nadeau, M. Sc.</font></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>
<font size="4" color="#3d85c6">Simon Nadeau, M. Sc.</font></div><div><font color="#3d85c6"><font size="3">Biologiste / Biologist</font></font></div><div><strong><font color="#007f00" size="3"></font></strong><br></div><div><div>Ressources naturelles Canada, Service canadien des forêts, Centre de foresterie des Laurentides / Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre</div><div>1055 rue du P.E.P.S., C.P. 10380 succ. Sainte-Foy, Québec (Québec), Canada G1V 4C7</div></div><div><a href="mailto:Simon.Nadeau.UBC@gmail.com" style="font-size:12.8000001907349px" target="_blank">Simon.Nadeau@a</a><span style="font-size:12.8000001907349px;color:rgb(0,0,255)"><a href="http://lumni.ubc.ca" target="_blank">lumni.UBC.ca</a>, </span><u style="color:rgb(0,0,255);font-size:12.8000001907349px"><div style="display:inline!important"><a href="mailto:Simon.Nadeau@RNCan-NRCan.gc.ca" target="_blank">Simon.Nadeau@canada.ca</a></div></u></div><div><span style="font-size:12.8000001907349px">Tel: (604) 349-5196</span><br></div></div></div></div></div></div></div></div></div></div></div></div>
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