Tutorial

Fast Matrix Algebra with LDGM Precision Matrices

To run these tutorials, first follow the installation instructions to clone the repo.

Using LDGMs with real data

To use LDGMs with real data, please consult ldgm/matlab/tutorials/realdata_tutorial.mlx.

This MATLAB Live Script shows how to:

1. Load LDGM precision matrices

2. Merge precision matrices with summary statistics

3. Estimate heritability

4. Compute polygenic scores

5. Perform basic matrix operations

6. Compute likelihood of the summary statistics

Simulating GWAS Summary Stats and running BLUPx

To use LDGMs to simulate GWAS summary statistics and run BLUPx, please consult: ldgm/matlab.tutorials/simulations_tutorial.mlx.

This script shows how to:

1. Load LDGM precision matrices

2. Simulate GWAS summary statistics with realistic LD patterns

3. Run BLUPxldgm on the summary statistics

4. Benchmark BLUPxldgm performance across populations