Exploring the effects of mitonuclear interactions on mitochondrial DNA gene expression in humans

This repository contains all the code generated for the manuscript.

doi: 10.3389/fgene.2022.797129

Edmundo Torres-González and Kateryna D. Makova*

*Correspondence to Kateryna D. Makova (kdm16@psu.edu)

Directory Structure

This repository contains the following directories:

1. mitonuclear_discordance: Includes all Python, R, and Bash scripts necessary for generating global ancestry estimates, mitochiondrial DNA haplogroup, and computing mitonuclear DNA discordance for each individual.

2. local_ancestry: Contains Bash and R scripts to generate local ancestry estimates using RFMix.

3. compare_local_and_global_ancestry: Contains Jupyter notebook that compares global genetic ancestry estimates to its equivalent when compiling local genetic ancestry estimates, as a sanity check.

4. Analysis: Contains the adjustment of gene expression for GTEx samples, local ancestry enrichment analysis, and the code utilized to generate plots for the manuscript.

Some key dependencies required for the analyses in this manuscript are:

• RFMix: estimates local genetic ancestry estimates.

• ADMIXTURE: estimates global genetic ancestry estimates.

• HaploGrep: profiles mitochondrial DNA haplogroup.