Getting Started in R (2025)
Thomas R. O’Neil
Last updated: 2025-02-04
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Knit directory: analysis-user-group/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | f654b8d | DrThomasOneil | 2025-02-04 | Build site. |
| Rmd | e6ea78d | DrThomasOneil | 2025-02-04 | wflow_publish(c("analysis/*.Rmd")) |
| html | 4968925 | DrThomasOneil | 2025-01-30 | Build site. |
| html | 299ff3d | DrThomasOneil | 2025-01-28 | Build site. |
| Rmd | 272b312 | DrThomasOneil | 2025-01-28 | wflow_publish(c("analysis/*")) |
| html | 023005d | DrThomasOneil | 2025-01-07 | Build site. |
| Rmd | 0ecb65d | DrThomasOneil | 2025-01-07 | Updated Getting Started in R. Chapter 1 completed |
| html | c893d70 | DrThomasOneil | 2025-01-06 | Build site. |
| Rmd | 8eec2ce | DrThomasOneil | 2025-01-06 | Initial Deployment |
| html | 660b0f8 | DrThomasOneil | 2025-01-06 | Build site. |
| html | 2e79a1d | DrThomasOneil | 2025-01-06 | Build site. |
| Rmd | 451a21f | DrThomasOneil | 2025-01-06 | Initial Deployment |
| Rmd | 2eeb8dc | DrThomasOneil | 2024-12-26 | first draft |
This 10-chapter workshop series is designed to introduce users to R programming with a focus on bioinformatics workflows and reproducibility. It emphasizes the mindset shift required to transition from manual tools like Excel to programmatic data analysis.
Introduction: Shifting mindsets to programming
Goals:
Introduce programming concepts and the mindset behind programmatic
workflows.
• Transition from manual tools (e.g. Excel & Prism) to
programming-based workflows.
• Understand the concept of handling data using code.
• Learn to navigate directories and file paths programmatically.
• Emphasize reproducibility and structured workflows.
Chapter 1: Getting Started with R and RStudio
Goals:
Set up R and RStudio, and get familiar with the interface.
• Understand what a programming language is.
• Know the difference between R, RStudio and python.
• Install R and RStudio.
• Exploring the interface – Console, Environment, Scripts.
• Installing and loading packages.
• Start your first project.
Chapter 2: Data Types and Structures
Goals:
Learn about data types and structures in R.
• Basic data types: numeric, character, logical.
• Data structures: vectors, matrices, data frames, lists.
• Assessing and querying data types and structures.
• Importing data (RDS, Excel, CSV files).
Chapter 3: Basic Programming
Goals:
Understand programming logic for automating tasks.
• Variables and assignments.
• Conditional statements (if, else).
• Loops (for, while).
• Writing functions.
Coming Soon
Chapter 4: Data Manipulation with
tidyverse
Goals:
Introduce tidyverse for filtering, mutating, summarizing
and pivoting data.
• Filtering rows (filter()), selecting columns
(select()). • Adding new columns (mutate()).
• Grouping and summarizing (group_by() +
summarize()). • Pivot longer and Pivot wider
Chapter 5: Visualization with ggplot2 – Part
1
Goals:
Create and customize visualizations using ggplot2.
• Basics of ggplot2
• Make a scatterplot, boxplot and column graph
• Customise labels, themes, and colors.
Chapter 6: Advanced Visualization with ggplot2
– Part 2
Goals:
Learn additional visualisation techniques.
• Adjusting theme elements
• Annotating the plots
• facet_wrap() and grid_plot()
• Savings plots
Chapter 7: Statistical Analysis
Goals:
Apply simple statistic to the synthetic data.
• Descriptive statistics: mean, median, mode.
• Hypothesis testing (t-tests, ANOVA).
• Correlation and regression.
Chapter 8: Reproducible Reports with RMarkdown
Goals:
Build a dynamic and shareable report of your analysis.
• Introduction to RMarkdown.
• Combining text, code, and visuals.
• Generate tables with knitr.
• Editing the yaml for additional customisations.
• Exporting to PDF and HTML.
Conclusions
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.3
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Australia/Sydney
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 httr_1.4.7 cli_3.6.3 knitr_1.49
[5] rlang_1.1.4 xfun_0.50 stringi_1.8.4 processx_3.8.4
[9] promises_1.3.2 jsonlite_1.8.9 glue_1.8.0 rprojroot_2.0.4
[13] git2r_0.35.0 htmltools_0.5.8.1 httpuv_1.6.15 ps_1.8.1
[17] sass_0.4.9 fansi_1.0.6 rmarkdown_2.29 tibble_3.2.1
[21] jquerylib_0.1.4 evaluate_1.0.1 fastmap_1.2.0 yaml_2.3.10
[25] lifecycle_1.0.4 whisker_0.4.1 stringr_1.5.1 compiler_4.4.0
[29] fs_1.6.5 pkgconfig_2.0.3 Rcpp_1.0.13-1 rstudioapi_0.17.1
[33] later_1.4.1 digest_0.6.37 R6_2.5.1 utf8_1.2.4
[37] pillar_1.9.0 callr_3.7.6 magrittr_2.0.3 bslib_0.8.0
[41] tools_4.4.0 cachem_1.1.0 getPass_0.2-4 
