README.md

Introduction

This site contains the materials for an R course run by Peter Mac.

This workshop is designed to provide beginners with foundational understanding of R programming language. Through a combination of theoretical explanations, hands-on coding exercises, and practical applications, participants will learn how to leverage R for data visualization of cancer biology datasets.

The workshop will cover essential programming concepts and gradually introduce more advanced topics, with a focus on using the ggplot2 package suite for data visualization. The aim of this workshop is to analyse data and create informative plots.

Instructor

Sandun Rajapaksa

Learning Objectives

Participants will gain the following skills:

• Proficiency in using R and RStudio for data analysis.
• Basic R programming skills.
• Reading datasets using readr package.
• Creating various types of plots using ggplot2 package.

Data

The Metabric study characterized the genomic mutations and gene expression profiles for 2509 primary breast tumours. In addition to the gene expression data generated using microarrays, genome-wide copy number profiles were obtained using SNP microarrays. Targeted sequencing was performed for 2509 primary breast tumours, along with 548 matched normals, using a panel of 173 of the most frequently mutated breast cancer genes as part of the Metabric study.

Refrences:

• Curtis et al., Nature 486:346-52, 2012
• Pereira et al., Nature Communications 7:11479, 2016

Both the clinical data and the gene expression values were downloaded from cBioPortal.

We excluded observations for patient tumor samples lacking expression data, resulting in a data set with fewer rows.

Credits and Acknowledgement

Credits and Acknowledgement

^These content were adapted from the Introduction to R: exploring the tidyverse course materials.^

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