<div dir="ltr">Indeed. I was using the github version of adegenet 2.0.0. After reinstalling the package directly, method# 1 is now working.<div><br></div><div>Thanks</div><div>V</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jul 28, 2015 at 11:08 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">
<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Hmmm... weird.
<br>
<br>
Method #2 will not work, but #1 should. Can you try this and tell us what you get:<br>
<br>
<font face="Courier New">library(adegenet)<br>
data(nancycats)<br>
nancycats[loc=-1]<br>
</font><br>
<div>One possibility is that your adegenet 2.0.0 was the old from github. So maybe trying again after<br>
<br>
<font face="Courier New">install.packages("adegenet") </font><br>
<br>
would be worth a try?<br>
Cheers<br>
Thibaut<br>
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<div style="direction:ltr"><font face="Tahoma" color="#000000" size="2"><b>From:</b> Vikram Chhatre [<a href="mailto:crypticlineage@gmail.com" target="_blank">crypticlineage@gmail.com</a>]<br>
<b>Sent:</b> 28 July 2015 15:52<br>
<b>To:</b> <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Cc:</b> Jombart, Thibaut<br>
<b>Subject:</b> Re: [adegenet-forum] How can I filter out loci out of HWE from a genind object?<br>
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<div dir="ltr">Hi Thibaut,
<div><br>
</div>
<div>This does not seem to work. Perhaps I am doing something wrong. Here is an example:</div>
<div><br>
</div>
<div>head(locNames(mygenind))</div>
<div>[1] "loc_121" "loc_229" "loc_472" "loc510" "loc688"</div>
<div><br>
</div>
<div>## Method 1</div>
<div>rmloci <- c(1,3)</div>
<div>mygenind2 <- mygenind[loci=-rmloci]</div>
<div>Warning message:</div>
<div>In .local(x, i, j, ..., drop = drop) :</div>
<div> the following specified loci do not exist: -1the following specified loci do not exist: -3</div>
<div><br>
</div>
<div>## Method 2</div>
<div>rmloci2 <- c("loc_121","loc_472")</div>
<div>mygenind2 <- mygenind[loci=-rmloci2]</div>
<div>Error in -rmloci : invalid argument to unary operator<br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">sessionInfo()</div>
<div class="gmail_extra">adegenet_2.0.0</div>
<div class="gmail_extra">ade4_1.6-2</div>
<div class="gmail_extra">R 3.1.2</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Thanks</div>
<div class="gmail_extra">V</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jul 28, 2015 at 10:31 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">Hi there,
<br>
<br>
this is easy to do since adegenet 2.0.0. You can use x[loc=...] where ... is any usual subsetting, which will be matched against locNames(x). You can use it to retain relevant loci, or discard the unwanted ones.<br>
<br>
For instance:<br>
<font face="Courier New"><br>
> library(adegenet)<br>
Loading required package: ade4<br>
<br>
/// adegenet 2.0.0 is loaded ////////////<br>
<br>
> overview: '?adegenet'<br>
> tutorials/doc/questions: 'adegenetWeb()' <br>
> bug reports/feature resquests: adegenetIssues()<br>
<br>
<br>
> data(nancycats)<br>
<b>> locNames(nancycats)<br>
[1] "fca8" "fca23" "fca43" "fca45" "fca77" "fca78" "fca90" "fca96" "fca37"<br>
</b><br>
<b>## removing loci 2, 4 and 5</b><br>
> toRemove= c(2,4,5)<br>
> x=nancycats[loc=-toRemove]<br>
> x<br>
/// GENIND OBJECT /////////<br>
<br>
// 237 individuals; 6 loci; 76 alleles; size: 102.9 Kb<br>
<br>
// Basic content<br>
@tab: 237 x 76 matrix of allele counts<br>
@loc.n.all: number of alleles per locus (range: 8-18)<br>
@loc.fac: locus factor for the 76 columns of @tab<br>
@all.names: list of allele names for each locus<br>
@ploidy: ploidy of each individual (range: 2-2)<br>
@type: codom<br>
@call: .local(x = x, i = i, j = j, loc = ..1, drop = drop)<br>
<br>
// Optional content<br>
@pop: population of each individual (group size range: 9-23)<br>
@other: a list containing: xy <br>
<br>
<b>## note the difference from locNames(nancycats):</b><br>
<b>> locNames(x)</b><br>
<b>[1] "fca8" "fca43" "fca78" "fca90" "fca96" "fca37"</b><br>
</font><br>
<br>
Cheers<br>
Thibaut<br>
<br>
<div><br>
<div style="font-family:Tahoma;font-size:13px">
<div><font size="2"><span style="font-size:10pt">
<div> <br>
==============================<br>
Dr Thibaut Jombart<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - School of Public Health<br>
Norfolk Place, London W2 1PG, UK<br>
Tel. : 0044 (0)20 7594 3658<br>
<a href="http://sites.google.com/site/thibautjombart/" target="_blank">http://sites.google.com/site/thibautjombart/</a><br>
<a href="http://sites.google.com/site/therepiproject/" target="_blank">http://sites.google.com/site/therepiproject/</a><br>
<a href="http://adegenet.r-forge.r-project.org/" target="_blank">http://adegenet.r-forge.r-project.org/</a><br>
Twitter: @thibautjombart<br>
<br>
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<div style="direction:ltr"><font face="Tahoma" color="#000000" size="2"><b>From:</b>
<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org" target="_blank">
adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<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 Ana Verissimo [<a href="mailto:verissimoac@gmail.com" target="_blank">verissimoac@gmail.com</a>]<br>
<b>Sent:</b> 20 July 2015 15:58<br>
<b>To:</b> <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> [adegenet-forum] How can I filter out loci out of HWE from a genind object?<br>
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<div></div>
<div>
<div dir="ltr">Hi all,
<div><br>
</div>
<div>I have a data set comprised on 1000s of SNP loci genotyped for 10s of individuals. I have tested loci for conformance to HWE and want to filter out those loci out of HWE. </div>
<div><br>
</div>
<div>Is there a function already available to perform this filtering in genind objects? </div>
<div>If not, I am guessing I may need to figure out a way to subset my data using a list of loci that I want to keep?</div>
<div><br>
</div>
<div>Any tips or suggestions are welcome! <br clear="all">
<div>Ana</div>
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