LinkageModel

This repository contains the following python files.

Grid_Search_Linkage.py: Code to calculate the MLE for the ancestry in the Linkage Model for arbitrary many chromosomes.
Test_whole_Population.py : Code to apply the statistical test with H0: The user should apply the Admixture Model vs. H1: The user should use the Linkage Model to real data.

Additionally, it contains

1000G_AIMsetKidd.vcf: example data, which have the correct format for the statistical test. These are the 1000 Geneomes Data taken from the GitHub page from Peter Pfaffelhuber.

The folder Evaluation consists of code that has been used to evaluate the methods. This includes : Code to evaluate the statistical test.
cM_calculateion.py: Code to calculate the differences between two loci in centi-Morgan.

Application of the code

To apply the code, please download the files and run them in e.g. spyder.

Example Output of the code

The example output of the code can be viewed as a comment in the code.