Thanks, Ben!  That worked.  I will join r-sig-phylo, I didn't know it was
there.

James

On Fri, Jan 28, 2011 at 1:46 PM, Ben Bolker <bbolker@gmail.com> wrote:

> James Meadow <jfmeadow <at> gmail.com> writes:
>
> >
> > Hi,
> >
> > I am trying to work with the ape package, and there is one thing I am
> > struggling with.  When calling the *read.GenBank()* function, I can get
> it
> > to work with an object created like this:
> >
> > *>x <- c("AY395554","AY611035", ...)*
> > *>read.GenBank(x)*
> >
> > However, I am trying to use the function to fetch several hundred
> sequences
> > at once.  So I have been testing with small files, but cannot get the
> right
> > format.  I tried to enter accession numbers with or without headers as a
> > .csv and just as a text file, and I have tried *as.vector*, but I always
> get
> > this error:
> >
> > >*x <- read.csv("numbers.csv",head=T)*
> > *>attach(x)*
> > *>x.vect <- as.vector(t(x)**)*
> > *>x.seqs <- read.GenBank(x.vect)*
> >
> > Error in FI[i]:LA[i] : NA/NaN argument
> >
> > I have been trying this with an identical set of accession numbers, and
> it
> > always works with the c() vector but not with the table, so the content
> is
> > not the problem.  I assume I am just missing a simple data structure
> detail,
> > but I am at a loss.  I have even tried a c() vector of more than a
> hundred
> > accession numbers, and it worked quite well, so the length is not a
> > problem.
>
> It's not entirely clear how your CSV file is structured, but I'm supposing
> that you have all your accession numbers in a single row (with
> appropriately
> matching headers).  (It would be a little bit more "R-ish" if you had
> them all in a column, and would make life a little easier, but let's
> work with what you have.)
>
> After you use read.csv(), try str(x)
>
> This should tell you that you have a data frame with a lot of columns,
> each of which is a factor with a single element and a single level.
>
> >From there try
>
> m <- as.matrix(x)
>
> str(m) should tell you you have a 1-row matrix of type 'character'
>
> then
>
> v <- c(m)
>
> should drop the dimensions and leave you with a character vector
> (try str(v) again to be sure)
>
> then
>
> read.GenBank(v)
>
> should work
>
> For future phylogenetic/comparative-methods type questions,
> it's probably better to write to the r-sig-phylo mailing list ...
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
James Meadow
Land Resources and Environmental Sciences
Montana State University
(406) 370-7157
jfmeadow@gmail.com

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