<div dir="ltr">Hi Gary, <div><br></div><div>it is not the first time we see discrepancies in F stats across different packages and estimators. As these are related to pegas and hierfstat, maybe you'll get better feedback posting it as an issue on the github project pages? I think Jérome and Emmanuel are on the adegenet forum, but they may miss this.</div><div><br></div><div>Best</div><div>Thibaut </div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology, Imperial College London<br>Head of RECON: <a href="http://repidemicsconsortium.org" target="_blank">repidemicsconsortium.org</a><br>WHO Consultant - outbreak analysis</div><div><a href="https://thibautjombart.netlify.com" target="_blank">https://thibautjombart.netlify.com</a><br>Twitter: @TeebzR<br>+44(0)20 7594 3658</div></div></div></div>
<br><div class="gmail_quote">On 13 April 2018 at 00:09, Gary Longo <span dir="ltr"><<a href="mailto:garycharleslongo@gmail.com" target="_blank">garycharleslongo@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi Thibaut and company!</div><div><br></div><div># I've noticed differences with Fst and Fis calculations in Pegas vs Hierfstat while using Adegenet</div><div><br></div><div>> data("nancycats")</div><div><br></div><div># using weir and cockerham in pegas</div><div>> nancycats_Fstat_as_loci <- Fst(as.loci(nancycats))</div><div>> nancycats_Fstat_as_loci</div><div><br></div><div> Fit Fst Fis</div><div>fca8 0.2447420 0.10146648 0.159454807</div><div>fca23 0.1646295 0.06746762 0.104191391</div><div>fca43 0.1514487 0.06893755 0.088620458</div><div>fca45 0.1010807 0.09792456 0.003498722</div><div>fca77 0.2790495 0.10036588 0.198618075</div><div>fca78 0.1842490 0.07025915 0.122603911</div><div>fca90 0.2098744 0.09168833 0.130116240</div><div>fca96 0.2034755 0.10744024 0.107595351</div><div>fca37 0.2604033 0.06985321 0.204860244</div><div><br></div><div># also using weir & cockerham in hierfstat</div><div>> nancycats_hfstat <- genind2hierfstat(nancycats)</div><div>> nancycats_wc <- wc(nancycats_hfstat)</div><div>> nancycats_wc_loci_stats <- as.data.frame(nancycats_wc[["<wbr>per.loc"]])</div><div>> nancycats_wc_loci_stats</div><div><br></div><div> FST FIS</div><div>1 0.10150515 0.148673460</div><div>2 0.06746762 0.104191391</div><div>3 0.06893755 0.088620458</div><div>4 0.07652596 -0.001451681</div><div>5 0.10036588 0.198618075</div><div>6 0.07025915 0.122603911</div><div>7 0.09168833 0.130116240</div><div>8 0.10981110 0.094857474</div><div>9 0.06985321 0.204860244</div><div><br></div><div><br></div><div>> colSums(<a href="http://is.na" target="_blank">is.na</a>(nancycats_<wbr>hfstat))</div><div> </div><div> pop fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37 </div><div> 0 20 0 0 21 0 0 0 9 0 </div><div><br></div><div><br></div><div>The results are identical in loci that are not missing data but are different in loci with missing data. </div><div><br></div><div>Two questions:</div><div>1) How are they handling missing data differently since they are both using Weir and Cockerham 1984? Follow up: which is better suited for calculating Fst and Fis values when there are missing data? I'm analyzing a SNP dataset based on ~2100 RADseq loci in over 500 individuals, which of course has some missing data at most loci. My results from calculating these values in Pegas vs Hierfstat are very different. Specifically Fst and Fis values are generally much higher and I don't get any negative Fis values when calculated in pegas. </div><div><br></div><div>2) Why does the conversion to hierfstat result in the loss of loci name? This would be very useful to retain for downstream comparisons.</div><div><br></div><div>Cheers,</div><div>Gary</div><span class="HOEnZb"><font color="#888888"><div><br></div><div><br></div>-- <br><div class="m_-663108442299344198gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Gary Charles Longo</div><div dir="ltr">NRC Research Associate</div><div dir="ltr">NOAA, National Marine Fisheries Service</div><div dir="ltr">2725 Montlake Blvd E</div><div dir="ltr">Seattle, WA 98112</div><div dir="ltr"><a href="http://garycharleslongo.wordpress.com" target="_blank">garycharleslongo.wordpress.com</a></div>(831) 247-3056</div></div></div></div></div></div></div>
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