stevenliuyi / admix Goto Github PK

This is an old project, but I was interested to know if there is more information related to the ML model used: a publication, or a more detailed description of the philosophy behind the model?

Thanks.

Hi,

Thanks for this fantastic project. I have a population allele frequency matrix that looks like the following matrix.

I would like it to perform admixture analysis, and this can't be directly converted into the *.alleles format since I don't have genotype data, but I can make an *.F file.

I would appreciate it if you could advise on how to perform that, and if there are code changes, I would really appreciate your pointing me to the code locations that need to be changed.

I checked #2 , and it solves one part of my problem.

Thank you,
Mo

Hi,

I have stumbled upon an issue with some FTDNA and Ancestry files. Whatever the model used, the calculator returns the following error:

/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/optimize/_minimize.py:324: RuntimeWarning: Method BFGS cannot handle constraints nor bounds. RuntimeWarning)
In addition, the percentage returned is the same for each reference population.

Note this is on OSX and the input files do not appear to be out of the ordinary.

Has anyone experienced a similar issue and been found a solution? I have to admit that I am rather ignorant when it comes to scipy and numpy.

Many thanks for your help.

How do I use this repo to make an admixture calculation with my own reference populations? Thanks!