<div dir="ltr"><div>Hi Samuel,<br><br></div><div>The tab function simply gives back a matrix of allele counts (for a genlight object). It won't replace the values IN the genlight object (since R is side-effect free). <br><br></div><div>Because of the way a genlight object works, you can't replace the values with the average counts of alleles, so what you might want to do is to use `tab()` to get the allele matrix with missing replaced with the mean value and then use `celing()` on that matrix to transform the average values to the nearest allele copy number (note: you could also use `round()`, but this will always round to the nearest even digit). From there, you can convert back to a genlight with the missing values replaced. <br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 4, 2019 at 11:00 AM <<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">adegenet-forum-request@lists.r-forge.r-project.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send adegenet-forum mailing list submissions to<br>
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1. Replacing NAs in genlight object (Samuel Weaver)<br>
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Message: 1<br>
Date: Sun, 3 Mar 2019 12:53:16 -0600<br>
From: Samuel Weaver <<a href="mailto:weave271@umn.edu" target="_blank">weave271@umn.edu</a>><br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: [adegenet-forum] Replacing NAs in genlight object<br>
Message-ID:<br>
<CAAeinLC0PVGsy7wrXdSrJLv7wDogqdiXvF+8FH3SPC=<a href="mailto:enha-qA@mail.gmail.com" target="_blank">enha-qA@mail.gmail.com</a>><br>
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<br>
I'm trying to change NAs in my dataset to the mean allele frequency to run<br>
various PopGen analyses through adegenet, but have been having trouble.<br>
Commands start below.<br>
<br>
Data<-vcfR2genlight(MyVcf)<br>
Data<br>
/// GENLIGHT OBJECT /////////<br>
<br>
// 11 genotypes, 5,467 binary SNPs, size: 877.8 Kb<br>
7647 (12.72 %) missing data<br>
<br>
// Basic content<br>
@gen: list of 11 SNPbin<br>
<br>
// Optional content<br>
@ind.names: 11 individual labels<br>
@loc.names: 5467 locus labels<br>
@chromosome: factor storing chromosomes of the SNPs<br>
@position: integer storing positions of the SNPs<br>
@other: a list containing: elements without names<br>
<br>
I then try to run the command listed in the tutorial and elsewhere on the<br>
forum, which is as follows:<br>
<br>
tab(Data, NA.method="mean").<br>
<br>
This, however, does nothing to replace the NA values in the original "Data"<br>
genlight object. I've looked for hours on how to do this with no avail, so<br>
any help would be greatly appreciated.<br>
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</blockquote></div>