Hello, thank You very much, Emmanuel, this worked perfectly. Silly me I've overlooked that. Yes, for microsatellites would be probably better use poppr's bruvo dist or ade4's dist.genet. Sincerely, Vojtěch PS: Later yesterday I have received spam answering my original post. Spammer is obviously subscribed and harvesting mails passing through the conference and then mailing users off-list. I've notified admins, but it's hard to resist such... ehm...
Dne Čt 21. ledna 2016 17:15:48 jste napsal(a):
> Hi Vojtěch,
>
> The trouble comes from boot.phylo() which resamples the columns of the
> data matrix with replacement: this may result in a bootstrap sample
> without population column and loci2genind() doesn't like it. The trick
> is to delete this column from the original "loci" object, and then
> reassign it within the estimation process so that loci2genind() works.
>
> pop <- LOCI$population
> LOCI$population <- NULL
>
> foo <- function(X) {
> X$population <- pop
> nj(dist(loci2genind(X)))
> }
>
> Then the following should work:
>
> NJ <- foo(LOCI)
> BOOT <- boot.phylo(phy=NJ, x=LOCI, FUN=foo, B=1000)
>
> BTW, I don't know if using dist() on a "genind" object is something
> really meaningful. Maybe you want to use another distance function from
> adegenet or another packae (eg, poppr). Anyway, the above trick will be
> useful in all cases since nj() only needs a distance matrix.
>
> Best,
>
> Emmanuel
>
> Le 21/01/2016 14:30, Vojtěch Zeisek a écrit :
> > Hello,
> > I have probably very simple problem, but I can't find the solution... :-(
> > I
> > wish to make bootstraped tree of attached microsatellite diploid data. It
> > works fine with DNA sequences and I was using same code last year and it
> > was working. :-)
> >
> > library(pegas)
> > library(ape)
> > LOCI <- read.loci("ssrs.txt", header=TRUE, loci.sep="\t", allele.sep="/",
> > col.pop=2, col.loci=3:14, row.names=1)
> > # Looks OK
> > GENIND <- loci2genind(LOCI)
> > DIST <- dist(x=GENIND, method="euclidean", diag=TRUE, upper=TRUE)
> > NJ <- nj(DIST)
> > BOOT <- boot.phylo(phy=NJ, x=LOCI, FUN=function(X)
> > nj(dist(loci2genind(X))), B=1000)
> >
> > |=
> > |
> > | 1%Error in df2genind(as.matrix(x[, attr(x, "locicol")]), sep =
> > | "[/\\|]",
> >
> > length of factor pop differs from nrow(X)
> >
> > Any idea what could went wrong?
> > Thank You,
> > Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/
Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ
http://www.ibot.cas.cz/en/
Czech Republic
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