seafloor / genetic_simulations

Genetic Simulations Tutorials - README

Project Overview

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

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Current Progress

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.

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Usage

To use these tutorials, you will need to have R installed on your machine along with the following packages:

• dplyr
• ggcorrplot
• 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.

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Requirements

R:

• tidyverse

Other:

• bcftools (Only needed for sampling from 1000 genomes remotely)

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Contributing

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.

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License

This project is open-sourced under the GPL-3.0 license. See the LICENSE file for more details.

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Note: This README is a living document and will be updated regularly to reflect the latest state of the project. Stay tuned for more!

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