twosamplemr 0.1.0

Two-sample Mendelian randomization implemented in Python

TwoSampleMR-Python

A package for performing Mendelian randomization using GWAS summary data. It allows causal inference using genetic variants as instrumental variables, fully integrated with the IEU OpenGWAS database.

This repository contains a reimplementation of the TwoSampleMR package.
It was developed as part of a master's thesis at UniZg-FER for academic purposes and learning.

Module	Description
instruments.py	Extracts instruments from OpenGWAS.
query.py	Queries outcome data from OpenGWAS.
harmonise.py	Harmonises exposure and outcome datasets.
mr.py	Core MR methods (IVW, Egger, Median, Mode, GRIP).
heterogeneity.py	Heterogeneity and pleiotropy tests.
multivariable_mr.py	Multivariable MR framework.

Example Usage:

from instruments import extract_instruments
from query import extract_outcome_data
from harmonise import harmonise_data
from mr import mr

exposure = extract_instruments(["ieu-a-2"])
outcome = extract_outcome_data(exposure["SNP"], ["ieu-a-7"])
dat = harmonise_data(exposure, outcome)
res = mr(dat)
print(res)