<html><head><base href="x-msg://65/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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></div><div>any idea?</div><div>Thanks!</div><div>Maria<br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>--</div><div>Maria Guerrina PhD</div><div><div>Università di Genova</div><div>DISTAV</div><div>Corso Dogali 1M</div><div>I - 16136 GENOVA (Italy)</div></div><div><a href="mailto:maria.guerrina@edu.unige.it">maria.guerrina@edu.unige.it</a></div><div><br></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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<br><div><div>On 23/nov/2015, at 13.11, Jombart, Thibaut wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div ocsi="0" fpstyle="1"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; ">Hello,<span class="Apple-converted-space"> </span><br><br>have you tried 'summary'? Note, the current devel version is better (previous summary was returning invisibly a list).<span class="Apple-converted-space"> </span><br><br>Cheers<br>Thibaut<br><div><br><div style="font-family: Tahoma; font-size: 13px; "><div class="BodyFragment"><font size="2"><span style="font-size: 10pt; "><div class="PlainText"><br></div></span></font></div></div></div><div style="font-family: 'Times New Roman'; color: rgb(0, 0, 0); font-size: 16px; "><hr tabindex="-1"><div id="divRpF89982" style="direction: ltr; "><font color="#000000" face="Tahoma" size="2"><b>From:</b><span class="Apple-converted-space"> </span><a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a><span class="Apple-converted-space"> </span>[adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Simon Nadeau [simon.nadeau.ubc@gmail.com]<br><b>Sent:</b><span class="Apple-converted-space"> </span>19 November 2015 23:00<br><b>To:</b><span class="Apple-converted-space"> </span><a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>[adegenet-forum] How to get observed heterozygosity per population<br></font><br></div><div></div><div><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><div><br></div><div>Thank you very much for your help,</div><div><br></div><div>Simon<br clear="all"><div><br></div>--<span class="Apple-converted-space"> </span><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 color="#3d85c6" size="4">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" target="_blank" style="font-size: 12.8px; ">Simon.Nadeau@a</a><span style="font-size: 12.8px; 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: 12.8px; "><span class="Apple-converted-space"> </span><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: 12.8px; ">Tel: (604) 349-5196</span><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>_______________________________________________<br>adegenet-forum mailing list<br><a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br><a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum</a></div></span></blockquote></div><br></div></body></html>