Hmm. I should try solutions before I post them. You need to make sure
that each tree in the list is of class phylo too. This works:
phylist<-read.tree(text="((((A:0.21,B:0.21):0.28,C:0.49):0.13,D:0.62):0.38,E:1.00);((((A:0.21,B:0.21):0.28,C:0.49):0.13,D:0.62):0.38,E:1.00);")
newnames<-c("G","H","I","J","K")
newlist <- lapply(phylist,
function(z) {
z$tip.label <- c("G","H","I","J","K")
class(z) <- "phylo"
z
})
class(newlist) <- "multiPhylo"
write.tree(newlist,file="newlist")
On Mon, 2008-09-01 at 10:55 +1000, Simon Blomberg wrote:
Try
class(newlist) <- "multiPhylo"
Then use write.tree.
Cheers,
Simon.
On Sun, 2008-08-31 at 20:39 -0400, [EMAIL PROTECTED] wrote:
> Hi all,
> I have hit an obstacle and I hope someone will know a quick fix. I
> want to read
> a list of trees, do something to those trees and then write them to a
> file. The list is seen as multiPhylo until I apply some function then
> it becomes a
> list that I cannot write to a file with write.tree. I put an
example below,
> where I read in two trees, and then use a function to change the
tip names and
> then try to write the trees to a file.
> Thanks in advance for your help!
> Stacey
>
> >
phylist<-read.tree(text="((((A:0.21,B:0.21):0.28,C:0.49):0.13,D:0.62):0.38,E:1.00);
> > ((((A:0.21,B:0.21):0.28,C:0.49):0.13,D:0.62):0.38,E:1.00);")
> > class(phylist)
> [1] "multiPhylo"
> > newnames<-c("G","H","I","J","K")
> > newlist <- lapply(phylist,
> + function(z) {
> + z$tip.label <- c("G","H","I","J","K")
> + z
> + })
> > write.tree(newlist,file="newlist")
> Error in write.tree(newlist, file = "newlist") :
> object "phy" is not of class "phylo"
>
> (and yes, write.tree did work on the multiphylo object before I did the
> function)
>
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> R-sig-phylo@r-project.org
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--
Simon Blomberg, BSc (Hons), PhD, MAppStat.
Lecturer and Consultant Statistician
Faculty of Biological and Chemical Sciences
The University of Queensland
St. Lucia Queensland 4072
Australia
Room 320 Goddard Building (8)
T: +61 7 3365 2506
http://www.uq.edu.au/~uqsblomb
email: S.Blomberg1_at_uq.edu.au
Policies:
1. I will NOT analyse your data for you.
2. Your deadline is your problem.
The combination of some data and an aching desire for
an answer does not ensure that a reasonable answer can
be extracted from a given body of data. - John Tukey.
