[adegenet-forum] adegenet-forum Digest, Vol 80, Issue 2

[Zhian Kamvar]

Hello,

I have solved this problem in the package "poppr" (http://cran.r-project.org/package=poppr). The function "aboot" will calculate bootstrapped nj and upgma trees for any genetic distance (http://rpackages.ianhowson.com/cran/poppr/man/aboot.html) (see the second example).

It doesn't do njs at the moment, but I can easily make a patch for that.

Cheers,
Zhian


> On Apr 7, 2015, at 03:00 , adegenet-forum-request at lists.r-forge.r-project.org wrote:
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> Today's Topics:
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>   1. conversion genind to loci (Virgilio Massimiliano)
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> 
> ----------------------------------------------------------------------
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> Message: 1
> Date: Mon, 6 Apr 2015 13:48:32 +0000
> From: Virgilio Massimiliano <massimiliano.virgilio at africamuseum.be>
> To: "adegenet-forum at lists.r-forge.r-project.org"
> 	<adegenet-forum at lists.r-forge.r-project.org>
> Subject: [adegenet-forum] conversion genind to loci
> Message-ID: <702BA0C8-1B27-4C0E-8E1C-41E36FADFB65 at africamuseum.be>
> Content-Type: text/plain; charset="utf-8"
> 
> hi,
> I?m trying to make a bootstrapped njt on msat data,
> as far as I can understand, it?s not possible to bootstrap my loci starting from a genind object and this:
> 
> myBoots <- boot.phylo(NJtree, data_genind at tab, B =100, function(xx)  njs(dist(xx)))
> 
> shouldn?t be correct as it bootstraps alleles (data_genind at tab)
> 
> 
> So I?m trying to convert my genind data into loci using genind2loci and read.loci :
> 
> 
> library(adegenet)
> data <- read.genetix("data.gtx")
> data_loci<-genind2loci(data)
> write.csv(data_loci, file = "data_loci.csv")
> library(pegas)
> data_pegas<-read.loci(file = "data_loci.csv", loci.sep = ",")
> 
> and then get the tree (based on Fst, but it doesn?t work either with distances)
> 
> pairFst <- pairwise.fst(data, res.type="matrix", truenames=TRUE)
> 
> library(ape)
> njtreFst_pop <- njs(pairFst)
> myBoots <- boot.phylo(njtreFst_pop, as.matrix(data_pegas), B = 3, function(xx)
>  njs(dist(xx)))
> 
> but it doesn?t seem to work (I?m attaching the input file) and I get only error messages no matter what I try...
> 
> What am I doing wrong? Is there a simpler way of getting bootstrapped msat loci starting form a genind object?
> 
> greeting and many thanks in advance
> 
> Massi
> 
> 
> 
> __________________________________
> Massimiliano Virgilio, PhD
> 
> Royal Museum for Central Africa
> 
> Joint Experimental Molecular Unit (JEMU)
> 
> Leuvensesteenweg 13, B-3080 Tervuren, Belgium, +32 (0) 27695366
> 
> massimiliano.virgilio at africamuseum.be<mailto:massimiliano.virgilio at africamuseum.be>
> 
> http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/
> 
> http://jemu.myspecies.info
> 
> 
> 
> 
> 
> 
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