Chapter 1 Getting Started with R and RStudio

1.1 A Beginner’s Guide for First-Year Graduate Students

1.2 What You’re Installing and Why

Before we start, here’s what each tool does:

R: The programming language that does the actual data analysis
RStudio: A user-friendly interface that makes R easier to use (like Microsoft Word for documents)
Git: Software that helps you download and sync course materials
Additional tools: Help R work with different types of data and create documents

Important: Install everything in the order listed below. Each step builds on the previous one.

1.3 Step 1: Install R

R is the programming language. Install this first!

1.3.1 For Windows:

Go to R Project website
Click “base” then “Download R for Windows”
Run the downloaded file and follow the installation prompts

1.3.2 For macOS:

These instructions work for ALL Macs (Intel and Apple Silicon):

Go to R Project website
Download the Intel (x86_64) version (yes, even for newer Macs with M1/M2/M3 chips)
Run the downloaded .pkg file and follow the installation prompts

1.4 Step 2: Install Additional Tools (macOS Only)

Windows users can skip to Step 3. Mac users need these tools for R to work properly:

1.4.1 Install Required System Tools:

Open Terminal (found in Applications → Utilities) and paste each command one at a time:

xcode-select --install

Click “Install” when prompted and wait for it to finish (this may take 10-15 minutes).

1.4.2 Install Graphics Support:

Go to XQuartz.org
Download and install XQuartz
Log out and log back in to your Mac after installation

1.4.3 Install Fortran Compiler:

Go to R Tools for macOS
Download gfortran-12.2-universal.pkg
Install it by double-clicking the downloaded file

1.4.4 Add Fortran to Your System Path:

In Terminal, paste these commands:

echo 'export PATH="/opt/gfortran/bin:/usr/local/bin:$PATH"' >> ~/.zshrc
echo 'export PATH="/opt/gfortran/bin:/usr/local/bin:$PATH"' >> ~/.bash_profile

Quit terminal and restart. In terminal, type:

gfortran --version

It should say GNU Fortran (GCC) 12.2.0. You’re all set.

1.5 Step 3: Install Git

Git helps you download and sync course materials.

1.5.1 For Windows:

Go to git-scm.com
Download Git for Windows
Run the installer using all default settings (just keep clicking “Next”)

1.5.2 For macOS:

If you completed Step 2, Git is already installed! To verify, open Terminal and type:

git --version

You should see version information.

1.5.3 Configure Git (All Users):

Open Terminal (Mac) or Git Bash (Windows) and run these commands with your information:

git config --global user.name "Your Full Name"
git config --global user.email "your.email@university.edu"

1.6 Step 4: Install RStudio

RStudio is the user-friendly interface for R.

Go to RStudio.com
Download RStudio Desktop (the free version)
Install it like any other program

1.6.1 For Mac Users with Apple Silicon (M1/M2/M3):

After installing RStudio:

In Finder, go to Applications
Right-click on RStudio.app
Select Get Info
Check the box “Open using Rosetta”

1.7 Step 5: Test Your Installation

Let’s make sure everything works:

1.7.1 Test RStudio and R:

Open RStudio (not R - always use RStudio)
You should see 4 panels:
- Console (bottom left) - this is where you type R commands
- Environment (top right) - shows your data
- Files/Plots (bottom right) - shows files and graphs
- Script (top left) - for writing longer code
Click in the Console (the bottom left panel where you see >)
Type this and press Enter:

2 + 2

You should see [1] 4

1.7.2 Test Git Connection:

In RStudio, go to File → New Project → Version Control
You should see “Git” as an option
If you see it, great! If not, restart RStudio and try again

1.8 Step 6: Download Course Materials

Now let’s get the main course files:

In RStudio, go to File → New Project → Version Control → Git
In the “Repository URL” field, paste:

https://github.com/gurinina/2025_IntroR_and_RStudio

Choose where to save the project on your computer
Click “Create Project”

RStudio will download all course materials. This may take a few minutes.

1.8.1 Additional Repositories:

As the course progresses, you may need to clone additional repositories for specific modules. Your instructor will provide those URLs when needed.

Tips: - To update materials later in the term, open the project and click the Pull button in the Git tab - To switch between projects later: RStudio → File → Open Project… and select the corresponding .Rproj file

1.8.2 Understanding the Git Pane:

When you open your course project in RStudio, you should see a tab labeled Git in the upper-right panel (next to Environment and History). This is where you can:

See changes you’ve made to files (they’ll appear in the list)
Revert changes if you made an edit you don’t want to keep
Pull to update your local copy with the newest course materials from GitHub
Push to send your own changes to GitHub (not applicable in this course — you won’t be pushing)

For this course, you will mainly use the Pull button (blue down-arrow icon) to update your files when the instructor posts new material.

1.8.3 IMPORTANT: Git Best Practices for Students

To avoid problems when updating course materials, follow these rules:

1.8.3.1 ✅ Safe Things to Do:

Create new files for your notes and practice work
Rename template files before editing them (like codebook_yourname.Rmd)
Make new folders like my_notes/ or homework/ for your work
Copy lesson files to a new name before modifying them

1.8.3.2 ⛔ Things That Cause Git Conflicts:

Don’t edit the original lesson .Rmd files directly
Don’t modify existing file names in the lessons folder
Don’t save your work in the main lesson directories

1.8.3.3 Golden Rule:

Never edit the original lesson files directly. Always create new files for your notes and practice. This way you can always Pull the latest updates without problems!

For the codebook: Copy 17-introR_codebook_template.Rmd and rename it to <lastname>_17-introR_codebook.Rmd (replace “lastname” with your actual last name). This file includes homework questions and space for your notes.

1.8.3.4 Suggested Workflow:

2025_IntroR_and_RStudio/
├── lessons/               # DON'T TOUCH - instructor files  
├── img/                   # DON'T TOUCH - course images
├── _book/                 # DON'T TOUCH - bookdown output
├── 17-introR_codebook_template.Rmd # DON'T EDIT - copy/rename instead
├── (other course files)   # DON'T TOUCH - various course materials
├── student_notes/             # YOUR FOLDER for notes
│   ├── <lastname>_17-introR_codebook.Rmd
│   ├── practice.R
│   └── other_notes.Rmd

1.9 Step 7: Install Required R Packages

R packages are like apps that add extra features. We need several for this course.

1.9.1 Important: Locate the Console First

Before running any code, you need to find the Console in RStudio:

Open RStudio
Look at the bottom left panel - this is the Console
You’ll see a > symbol - this is where you type R commands
Click in this area to make sure your cursor is active in the Console

1.9.2 COPY AND PASTE THIS CODE INTO THE CONSOLE:

Click in the Console (bottom left panel with the > symbol) and paste this entire block of code:

# Set CRAN mirror first (this tells R where to download packages)
options(repos = c(CRAN = "https://cloud.r-project.org/"))

# Install basic tools first
install.packages(c("BiocManager", "devtools", "ggraph", "tidyverse"))

# Install Bioconductor (for biological data analysis)
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

# Install all required packages for the course
BiocManager::install(c(
"apeglm", "bookdown", "clusterProfiler", "colorspace", "DESeq2", "details", "dplyr", "enrichplot", "fansi", "fgsea", "ggplot2", "ggrepel", "ggridges", "ggthemes", "gplots","GO.db", "GOSemSim", "igraph", "knitr", "org.Hs.eg.db", "patchwork", "pheatmap", "purrr", "RColorBrewer", "rmarkdown", "rsconnect", "scales",  "tidydr", "tidyr" ,"tidyverse", "tinytex",  "visNetwork"
))

# Install course-specific package
devtools::install_github("gurinina/GOenrichment", force = TRUE)

# Install document creation tools
if (!tinytex::is_tinytex()) {
    tinytex::install_tinytex(force = TRUE)
}

1.9.3 After Pasting the Code:

Press Enter to run all the commands
Be patient! This process takes 10-15 minutes and downloads many packages
Don’t worry about the scrolling text - this is normal
If prompted to install from source, type n and press Enter
If asked to restart R, type y and press Enter

1.10 Step 8: Verify Everything Works

Let’s test that all packages installed correctly.

1.10.1 COPY AND PASTE THIS TEST CODE INTO THE CONSOLE:

Again, click in the Console (bottom left panel) and paste this code:

# Check if key packages work
library(ggplot2)
library(dplyr)
library(DESeq2)

# If no error messages appear, you're ready!
cat("Success! All packages are working.\n")

If you see “Success! All packages are working.” then everything is installed correctly!

1.11 What Success Looks Like

✅ RStudio opens without errors
✅ You can type 2 + 2 in the Console and get [1] 4
✅ You have a folder with course materials from the main repository
✅ The test code runs without errors and shows “Success!”

1.12 Common Problems and Solutions

1.12.1 “Package not found” errors:

Make sure you’re typing in the Console (bottom left panel)
Try restarting RStudio and running the code again
Make sure you pasted the CRAN mirror line: options(repos = c(CRAN = "https://cloud.r-project.org/"))

1.12.2 “Command not found” in Terminal:

Close and reopen Terminal
Try restarting your computer

1.12.3 RStudio can’t find Git:

Make sure you installed Git before RStudio
Restart RStudio completely (quit and reopen)

1.12.4 Installation seems stuck:

Be patient! Package installation can take 15-30 minutes
As long as you see text appearing, it’s working

1.12.5 “trying to use CRAN without setting a mirror” error:

Make sure you ran the first line: options(repos = c(CRAN = "https://cloud.r-project.org/"))
Restart RStudio and try again

1.13 Getting Help

If something doesn’t work:

Try restarting RStudio
Try restarting your computer
Ask a classmate or instructor
Email the instructor with:
- What step you’re on
- What error message you see (copy and paste it)
- A screenshot if helpful

Remember: Software installation can be tricky, even for experienced users. Don’t worry if you need help - this is completely normal!

1.14 Next Steps

Once everything is installed:

Explore RStudio - click around and see what’s in each panel
Try the built-in R tutorial: In the Console, type:

install.packages("swirl")
library(swirl)
swirl()

Read the course materials you downloaded
Don’t panic! Learning R takes time, and everyone starts as a beginner

Welcome to R! You’re ready to start your data analysis