Julian
Since no one has answered this all day I will tell you how I would do it.
Basically what you want to do is subset your data and keep only the taxa
whose names are not found on your list of bad taxa. This is a pretty
straightforward problem of subsetting your data. Here is a four line
solution to your problem:
alignment <- read.FASTA("dna.fasta") ## read the alignment
bad.taxa <- read.csv("rogues.csv",header=F)[,1] ## pull in the column of
csv with taxa names (I assume its column 1)
`%ni%` = Negate(`%in%`) ## create a
function "not an element in"
stable.taxa.alignment <- alignment[names(alignment) %ni% bad.taxa] ##
save only sequences != to rogues
hope this is helpful
cheers
On Tue, May 14, 2013 at 3:48 PM, Julian Aguirre-Santoro <
jaaguirr...@gmail.com> wrote:
> Dear all,
>
>
>
> I have a list of Rogue taxa that I want to remove from my dataset in
> order to improve the support of my phylogenetic hypothesis. I can´t figure
> out how to match that list of rogue taxa (which I have as a .csv file) with
> my original DNA sequence matrix (which I have as DNAbin object), so that I
> can remove the problematic species and realign my sequences again.
>
>
>
> Thank you!
>
>
>
> Julián
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>
>
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