a program to model admixture using marker genotype data
Are there any differences between the Windows and Linux versions?
No. They are identical, just compiled for different platforms.
Is there a Windows interface / GUI ?
No. An early version had a WIndows frontend but we are no longer using this. The console version runs fine under Windows.
Is there a version for UNIX?
There is no precompiled version for UNIX but you can easily compile one yourself. Instructions on how to obtain and compile the source code are here.
Will it work with a different processor?
Probably. If not, you can compile a version optimised for your platform. See instructions here.
The program won't run !
Check you have execute permission for the executable (ls -l admixmap). If not, use the command chmod +ux.
The program has crashed !
Examine any error messages and ensure the options are valid. If it still won't run, send us the data and the exact options you are using and include any error messages.
What is best way to put in the genotypes from the gene we want to test for association with is. Is it okay to put them in the genotypes file? And how should it be declared in the locus file?
ADMIXMAP makes no distinction between markers and candidate loci. All loci are tested for association.
Should we specify ancestral frequencies where they are available or should we not specify and let the program do its analysis anway?
In the prior allele frequency file, enter 0.5 (reference prior) for cells where you have no allele frequency data from the parentals.
Can I use microsatellite data?
Yes. Code the different alleles as integers from 1 to the number of alleles.
When should I use a correlated allele frequency model?
The correlatedallelefreqs option should be used only if you are unable to supply priors on the ancestry-specific allele freqs. Specifying this option introduces another layer into the model - instead of a prior on the allele frequencies, the allele frequencies are modelled as drawn from a Dirichlet distribution parameterized as (p, eta) where p is a proportion vector (varies across loci) and eta is the dispersion parameter (same for all loci). This helps the program to infer subtle stratification/admixture, but should be used only as a last resort when prior information on the allele freqs is not available.
How do I specify a prior for the dispersion parameter in a dispersion ('historicallelefreqs') model?
The mean and variance you specify for eta should reflect your subjective evaluation of the range of values that are plausible. If you are unsure, you can use the default.
Error message #1:
'R' is not recognized as an internal or external command, operable program or batch file.
You need to put the path to R in your PATH environment variable. Instructions on how to do this are in the manual.
Error message #2:
unable to open input file
R cannot find the script. Check the path to the script (relative to the working directory) is correct. The simplest arrangement is to have the perl script, R script and executable all in the same place, one level above a subdirectory for results.
Error message #3:
Error in xy.coords(x, y, xlabel, ylabel, log) : (subscript) logical subscript too long Execution halted
Probably a bug. Send us your output and we'll try to fix it.
Error message #4:
Error in FUN(newX[, i], ...) : 'x' is empty
R is trying to read an empty file. You are probably using an old version of the R script. Get the latest version and if the problem persists, let us know.
Error message #5:
Error in file(file, "r") : unable to open connection
R cannot find your results. Check your paths are correct.
The R script crashes when reading large output files. Are they too big?
Try increasing R's memory limit using the function memory.limit or the command-line argument max.-memory-size. If this doesn't work try thinning the output by specifying a larger value of every.
How do I view the graphical output?
You need a postscript viewer e.g Ghostview.
How do I get pdf format graphics?
You need to convert the postscript files produced by the script. To do this in Ghostview, press F and select pdfwrite (the default).
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