a program to model admixture using marker genotype data
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Installing and running the program
ADMIXMAP runs as a console application. We are no longer supporting the Windows graphical front-end. Binaries (compiled executable files) are provided for Linux and Windows via SourceForge.
The source code is available as a tarball from the same page. Compilation instructions are provided. The source code is also available from our Subversion repository. Instructions for accessing the repository are here.
If you have downloaded a binary, or compiled the program yourself, and placed the ADMIXMAP executable in a directory that lies on your search path, the program can be invoked directly by typing
where optionsfile contains statements of the form optionname=value, one line per optionname. A sample optionsfile, testArguments.txt is provided with the test files.
To generate summary statistics, tables and graphics from the output files generated by ADMIXMAP you will need to run the script AdmixmapOutput.R. This requires the R statistical package to be installed.
If your output files are in a directory other than 'results', you will need to supply R with the directory name. If running R interactively (Rterm, Rgui), use the command
Sys.putenv("RESULTSDIR" = <resultsdirname>)
If you are running the script from the command line, first set the RESULTSDIR environment variable.
To do this in Linux use: "export RESULTSDIR=resultsdirname"
and in Windows use: "set RESULTSDIR=resultsdirname"
Then run the R script using:
R --quiet --no-save --no-restore <AdmixmapOutput.R >resultsdirname/Rlog.txt.
The most convenient way to run the entire analysis is to use a Perl script. If you are working in Windows, you should install ActivePerl if not already installed. The Perl script specifies the user options, writes the to file, runs ADMIXMAP, and invokes R in batch mode to run the script AdmixmapOutput.R to process the output files. See, for example, the Perl script admixmap.pl provided with the test files. User options can be changed by editing this file. This requires only minimal knowledge of Perl. The Perl script is especially convenient when running a batch of different analyses, as each run may require only a few options to be changed.
The Perl script admixmap.pl should be invoked from a directory that has a sub-directory named "data" containing the data files. Results will be output to the directory specified in the resultsdir option or to one named "results" if none is specified.
To construct the email addresses, append @ucd.ie
If you have problems running the program, please supply as much information as possible, including any on-screen error messages, the logfile and Rlog if available.
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