This website hosts R teaching materials for the Cleveland Clinic Molecular Medicine PhD program. The material will be split across 5 1-hour sessions as part of the Tools course, followed by 2 2-hour sessions as part of the Biostatistics and Epidemiology course.

Tools course

Session 1

• Introduction to the tools

  • R
  • RStudio
  • Posit Workbench

• Using RStudio

• Installing and loading R packages

  • CRAN
  • Github
  • Bioconductor

Session 2

• Loading data

  • .xlsx
  • .csv
  • Other formats
  • Variable names (janitor)

• Reproducibility

  • RStudio projects
  • Project workflow and organization
  • {here} package

Session 3

• Basic programming

  • Assigning objects
  • Functions
  • Getting help
  • The pipe operator
  • Testing for equality
  • Indexing
  • Subsetting

Session 4

• Manipulate dataframes

  • The dplyr package
  • Rename columns
  • Add columns
  • Group a continuous variable
  • Recategorize a categorical variable
  • Sort by row

Session 5

• Put it all together

Biostatistics and Epidemiology

Session 1

• Refresher of the Tools course material

  • R basics
  • Descriptive statistics

• Visualization

  • Scatterplot
  • Bar chart
  • Histogram
  • Line chart
  • Boxplot
  • Customization
  • Faceting
  • Saving plots

Session 2

• Adjustment for multiple comparisons

• Advanced programming

  • Writing custom functions
  • For loops/apply/map

• Statistical tests

  • Fisher’s exact test
  • Chi-squared test
  • Wilcoxon rank sum test/Kruskal-Wallis test
  • T-test
  • ANOVA
  • Wilcoxon signed rank test
  • Paired t-test