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

Tue Apr 7 17:57:33 CEST 2015

YES!
that was the bit I was missing,
many thanks for help
cheers
M.

__________________________________
 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

On 07 Apr 2015, at 16:57, Zhian Kamvar <zkamvar at gmail.com<mailto:zkamvar at gmail.com>> wrote:

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<mailto: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<mailto: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:

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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