Hi Christoph & Gustavo,
Quoting Christoph Heibl <christoph.he...@gmx.net>:
Hi Gustavo,
Hava a look at:
?`%in%`
Given a matrix 's' of class DNAbin and a tree 'tr' of class phylo, you
simply do:
s <- s[-(rownames(s) %in% tr$tip.label), ]
Yes but replace '-' with '!':
s <- s[!(rownames(s) %in% tr$tip.label), ]
'%in%' returns logical values which will be (silently) converted to
numeric by '-'. Another possibility is to use match:
s <- s[-match(tr$tip.label, rownames(s), ]
In both cases, you can select the dropped tips instead of deleting
them by removing the appropriate operator (! or -).
Of course this requires matching taxon names in s and tr...
That will certainly be the case if the tree has been estimated with R
(eg, nj() in ape or pml() in phangorn).
Emmanuel
HTH
Christoph
________________________________________________________
Christoph Heibl
Systematic Botany
Ludwig-Maximilians-Universität München
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D-80638 München
GERMANY
phone: +49-(0)89-17861-251
e-mail: he...@lmu.de
http://www.christophheibl.de/ch-home.html
SAVE PAPER - THINK BEFORE YOU PRINT
On Sep 28, 2009, at 7:43 AM, Gustavo Ybazeta wrote:
Hello,
I am working with a more less a big phylogeny (over 100 taxa). I had used
drop.tips to analyze some clades independently and produce sub-trees. My
question is: how can I use the information in the modified trees to drop the
same taxa in the original DNA matrix? I have been doing this
outside of R but
I am sure should be a better way to do this.
Thanks
Gustavo
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