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Setup

Environment Setup Guide

Before using this repo, complete the relevant steps in the environment setup guide, which installs the core tools you’ll need for this module:

  • Visual Studio Code
  • Git
  • Git Bash (for Windows)
  • Quarto
  • R
  • PLINK2

R Packages to Install (Run Once)

Open a Terminal and install the required packages:

R --vanilla -e "cran_packages <- c('data.table','ggplot2','seqminer','HardyWeinberg','dplyr','qqman','knitr','metafor'); missing <- setdiff(cran_packages, rownames(installed.packages())); if (length(missing)) install.packages(missing, repos='https://cloud.r-project.org')"

These packages cover the tutorials and assignment workflows in this repository.

Notes

  • This module uses command-line tools (especially plink2) in addition to R.
  • Tutorials and assignments use .qmd files, so Quarto should be installed and available.

Test Your Setup

Run these checks from the repository root to confirm your environment is ready.

  1. Verify command-line tools:
quarto --version
R --version
plink2 --version
  1. Verify required R packages:
R --vanilla -e "pkgs <- c('data.table','ggplot2','seqminer','HardyWeinberg','dplyr','qqman','knitr','metafor'); missing <- setdiff(pkgs, rownames(installed.packages())); if (length(missing)) { cat('Missing packages:\\n'); print(missing); quit(status = 1) } else { cat('All required packages are installed.\\n') }"
  1. Run a Quarto smoke test (no external data required):
printf '%s\n' '---' 'title: "setup-smoke-test"' 'format: html' '---' '' '```{r}' '1 + 1' '```' > setup_smoke_test.qmd
quarto render setup_smoke_test.qmd

If all checks pass without errors, your setup is complete.

For questions or issues, contact the learning support team or email courses.dsi@utoronto.ca.