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