fast-kernel-set-test 0.1.0

This is the package for various epistasis related softwares.

Fast Model-X Kernel-based Set Testing Toolkits

This folder has been updated with both the FastKAST and QuadKAST

Please check sub-branch for detailed instruction on each specific method.

Requirements

1. You need python >= 3.60 in order to run the code (anaconda3 recommended)
2. pip install .

You can either follow the standard pipeline FastKAST_annot.py and QuadKAST_annot.py, or import the neccessary function to build based on your own I/O.

Exmaple

To run the demo FastKAST code with a customized window size, you can generate a annotation file with "start_index end_index" as a row, and run

python FastKAST_annot.py --bfile ./example/sim --phen ./example/sim.pheno --annot ./example/sim.new.annot

Or directly run

sh run_rbf_annot.sh

To run the demo FastKAST code with a customized window size, you can generate a annotation file with "start_index end_index" as a row, and run

python QuadKAST_annot.py --bfile ./example/sim --phen ./example/sim.pheno --annot ./example/sim.new.annot

Or directly run

sh run_quad_annot.sh

Data availability

The detailed statistics used to generate the main table and the Venn diagram of the paper are provided in the Data folder

✅ Efficient multi-traits analysis (Sep 30, 2024)