<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style id="owaParaStyle" type="text/css">P {margin-top:0;margin-bottom:0;}</style>
</head>
<body ocsi="0" fpstyle="1">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi there,
<br>
<br>
please check the forum archives, this has been answered several times. I think I even mention it in the tutorial. You need to remove 'system.file' and just indicate the path to your file.<br>
<br>
Cheers<br>
Thibaut<br>
<div><br>
<div style="font-family:Tahoma; font-size:13px">
<div class="BodyFragment"><font size="2"><span style="font-size:10pt">
<div class="PlainText"> <br>
==============================<br>
Dr Thibaut Jombart<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - School of Public Health<br>
Norfolk Place, London W2 1PG, UK<br>
Tel. : 0044 (0)20 7594 3658<br>
http://sites.google.com/site/thibautjombart/<br>
http://sites.google.com/site/therepiproject/<br>
http://adegenet.r-forge.r-project.org/<br>
Twitter: @thibautjombart<br>
<br>
<br>
</div>
</span></font></div>
</div>
</div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF107527"><font face="Tahoma" color="#000000" size="2"><b>From:</b> adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Ella Bowles [ebowles@ucalgary.ca]<br>
<b>Sent:</b> 24 September 2015 20:07<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> [adegenet-forum] adegenet not recognizing file extensions<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">
<div class="gmail_default" style="font-size:large; color:rgb(0,0,255)">Hello,</div>
<div class="gmail_default" style="font-size:large; color:rgb(0,0,255)"><br>
</div>
<div class="gmail_default" style="font-size:large; color:rgb(0,0,255)">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</div>
<div class="gmail_default" style="font-size:large; color:rgb(0,0,255)"><br>
</div>
<div class="gmail_default" style=""><font color="#0000ff" size="4">data <- read.genetix(system.file("8c9.gtx", package = "adegenet"))</font><br>
</div>
<div class="gmail_default" style="font-size:large; color:rgb(0,0,255)"><br>
</div>
<div class="gmail_default" style="font-size:large; color:rgb(0,0,255)">for many different permutations of filetype. These include read.genepop for genepop files, read.structure for structure filies. I keep getting the error</div>
<div class="gmail_default" style="font-size:large; color:rgb(0,0,255)"><br>
</div>
<div class="gmail_default" style="font-size:large; color:rgb(0,0,255)">
<div class="gmail_default"> Converting data from GENETIX to a genind object... </div>
<div class="gmail_default">Error in if (toupper(.readExt(file)) != "GTX") stop("File extension .gtx expected") : </div>
<div class="gmail_default"> argument is of length zero</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">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?</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">With thanks,</div>
<div class="gmail_default">Ella</div>
</div>
<div><br>
</div>
-- <br>
<div class="gmail_signature">
<div dir="ltr">
<div>Ella Bowles<br>
PhD Candidate </div>
<div>Biological Sciences</div>
<div>University of Calgary<br>
<br>
e-mail: <a href="mailto:ebowles@ucalgary.ca" target="_blank">ebowles@ucalgary.ca</a>,
<a href="mailto:bowlese@gmail.com" target="_blank">bowlese@gmail.com</a></div>
<div>website: <a href="http://ellabowlesphd.wordpress.com/" rel="nofollow me" style="color:rgb(59,89,152); font-family:'lucida grande',tahoma,verdana,arial,sans-serif; font-size:11.2px; line-height:17px" target="_blank">http://<span style="display:inline-block"></span>ellabowlesphd.wordpre<span style="display:inline-block"></span>ss.com/</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>