ecielyang / ERStruct-matlab

A MATLAB toolbox for inferring the number of top informative PCs that capture population structure based on genotype information.

ERStruct

A MATLAB toolbox for inferring the number of top informative PCs that capture population structure based on genotype information.

Requirements for Data File

Data files must be of .mat format. The data matrix must with 0,1,2 and/or NaN (for missing values) entries only, the rows represent individuals and columns represent markers. If there are more than one data files, the data matrix inside must with the same number of rows (try splitting the data files into smaller ones if MATLAB returns an out of memory error).

Examples

Example data files test_chr21.mat and test_chr22.mat can be found on the ERStruct GitHub repository.

ERStruct(2504, '.', ["test_chr21","test_chr22"], 10000, 1e-4)

Other Details

Please refer to our paper An Eigenvalue Ratio Approach to Inferring Population Structure from Whole Genome Sequencing Data.