[adegenet-forum] adegenet not recognizing file extensions

[Ella Bowles]

Hello,

I'm trying to read files into adegenet and convert to genind objects, but
am getting an error. After I have correctly specified/set the directory
that the files are in I have used the line

data <- read.genetix(system.file("8c9.gtx", package = "adegenet"))

for many different permutations of filetype. These include read.genepop for
genepop files, read.structure for structure filies. I keep getting the error

 Converting data from GENETIX to a genind object...
Error in if (toupper(.readExt(file)) != "GTX") stop("File extension .gtx
expected") :
  argument is of length zero

The thing that I can see as the possible issue is that my files originally
had different extensions (from the populations program of stacks). They
were previously ".genepop" and ".strucuture", and I changed them manually
to the ".gen" and ".stru" suffixes. Can you see a way around this?

With thanks,
Ella

-- 
Ella Bowles
PhD Candidate
Biological Sciences
University of Calgary

e-mail: ebowles at ucalgary.ca, bowlese at gmail.com
website: http://ellabowlesphd.wordpress.com/
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