Programming and Tidy Data Analysis in R

These are the course notes for the Monash Data Fluency’s “Programming and Tidy data analysis in R” course. This is an intermediate level R workshop, for people wishing to increase their fluency in R. It covers tasks that while not specifically involved in statistical analysis are necessary when working with data: loading data and getting it into a form that is easy to work with, automating repetitive tasks, identifying problems such as the need for normalization and transformation, and properly understanding the story the data wants to tell.

Slides

• Introduction (.Rmd)

Topics

• Programming (.Rmd)
• Communicating your results (.Rmd)
• The Tidyverse: dplyr, ggplot2, and friends (.Rmd)

Setup

This workshop is designed to work Posit Cloud. Monash users can log in to Posit Cloud with their Monash google account. You can also use R and RStudio on your own laptop.

Create a new project, either in Posit Cloud or RStudio on your own laptop, then run the R code below. This will download files and install packages used in this workshop. If using R on your own laptop, then to use FastQC you will need to have installed Java, and the FastQC steps will probably need some adjustments for Windows computers (this isn’t an essential part of the workshop).

# Download workshop files
download.file(
    "https://monashdatafluency.github.io/r-progtidy/r-progtidy-files.zip",
    "r-progtidy-files.zip")
unzip("r-progtidy-files.zip")

# Download FastQC software
download.file(
    "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip",
    "fastqc_v0.11.8.zip")
unzip("fastqc_v0.11.8.zip")
system("chmod u+x FastQC/fastqc")

# Install tidyverse packages and rmarkdown
install.packages(c("tidyverse", "rmarkdown"))

# Optional: install some further packages 
# (these are mentioned but not essential to the workshop)
install.packages(c("devtools", "usethis", "BiocManager"))
BiocManager::install("edgeR")

Files

The workshop files downloaded by the setup instructions above are also available here:

• r-progtidy-files.zip

See also

• R workshop material from Monash Data Fluency
• Monash Data Fluency
• Monash Bioinformatics Platform
• Next steps

• “R for Data Science” by Garret Grolemund and Hadley Wickham
• Hadley Wickham’s website has further useful resources.
• The official R manuals give a complete description of the R language.

Authors

This course was developed by Paul Harrison and Richard Beare for Monash Data Fluency and the Monash Bioinformatics Platform.

This work is licensed under a Creative Commons Attribution 4.0 International License.

Source code

• GitHub repository