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 ... > > ______________________________________________ > 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 jfmea...@gmail.com [[alternative HTML version deleted]] ______________________________________________ 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.