Welcome to the Genetic Simulations Tutorials repository 👋
This project is a collection of R tutorials designed to guide you through various aspects of simulating genetic data, focusing on Single Nucleotide Polymorphisms (SNPs), Linkage Disequilibrium (LD) and espistasis. The tutorials are written in R Markdown (Rmd) format for now, but will ultimately be in quarto and available in both Python and R
Author: Matthew Bracher-Smith
Date Created: 25/01/2024
Status: Work in Progress
This repository is actively being developed. New tutorials and updates will be added as the project evolves. As of now, the tutorials cover:
- Simulating unassociated SNPs
- Additive liability-threshold models
- Multiplicative interaction models
- Generating simple LD
- Creating SNP data with varying LD patterns
- Simulating complex LD blocks
Each tutorial will include detailed explanations and R code snippets to demonstrate the concepts.
To use these tutorials, you will need to have R installed on your machine along with the following packages:
dplyrggcorrplot- Other dependencies may be required as the project grows
The tutorials are structured as R Markdown files. To view or run the tutorials, open the Rmd files in an R environment such as RStudio.
R:
- tidyverse
Other:
- bcftools (Only needed for sampling from 1000 genomes remotely)
As this is a work in progress, contributions, suggestions, and feedback are highly appreciated. If you have ideas for additional topics or improvements, please feel free to submit an issue or pull request.
This project is open-sourced under the GPL-3.0 license. See the LICENSE file for more details.
Note: This README is a living document and will be updated regularly to reflect the latest state of the project. Stay tuned for more!