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

[Zhian Kamvar]

Actually, about does work on populations if you give it a genpop object.

Cheers,
Zhian
> On Apr 7, 2015, at 07:53 , Virgilio Massimiliano <massimiliano.virgilio at africamuseum.be> wrote:
> 
> Hi Zhian,
> 
> many thanks for your answer,
> 
> The problem with aboot it that it calculates distances among individuals
> (and I have some 800 individuals) but not among populations.
> 
> The reason I was using pairwise.fst of adegenet was that it has a pop
> argument, similarly dist.genpop works with populations.
> 
> Or do you have a way of using aboot on populations?
> 
> Cheers 
> 
> M.
> 
> 
> On 07/04/15 16:10, "Zhian Kamvar" <zkamvar at gmail.com> wrote:
> 
>> 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 ,
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>>> Today's Topics:
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>>>  1. conversion genind to loci (Virgilio Massimiliano)
>>> 
>>> 
>>> ----------------------------------------------------------------------
>>> 
>>> 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 africa
>>> museum.be>
>>> 
>>> http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/
>>> 
>>> http://jemu.myspecies.info
>>> 
>>> 
>>> 
>>> 
>>> 
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>>> End of adegenet-forum Digest, Vol 80, Issue 2
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>> 
>