class: center, middle, inverse, title-slide # 7.1 Introduction to R and RStudio ## MICB 405 101 2021W1 Bioinformatics ### <a href="mailto:stephan.koenig@ubc.ca">Stephan Koenig</a> ### University of British Columbia ### February 17, 2022 --- <style>.shareagain-bar { --shareagain-foreground: rgb(255, 255, 255); --shareagain-background: rgba(0, 0, 0, 0.5); --shareagain-facebook: none; --shareagain-pinterest: none; --shareagain-reddit: none; }</style> ## Module outline - **Oct 26** Introduction to R and RStudio - **Oct 28** Differential analysis with DESeq2 - **Nov 2** R tidyverse: Wrangling data I - **Nov 4** R tidyverse: Wrangling data II - **Nov 9** R tidyverse: Visualizing data - **Nov 16** R Markdown: Reproducibility in R Most classes will be live-coding of R tutorials. All content in R tutorials is testable. On slides, testable content is indicated by a pencil <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:FireBrick;overflow:visible;position:relative;"><path d="M497.9 142.1l-46.1 46.1c-4.7 4.7-12.3 4.7-17 0l-111-111c-4.7-4.7-4.7-12.3 0-17l46.1-46.1c18.7-18.7 49.1-18.7 67.9 0l60.1 60.1c18.8 18.7 18.8 49.1 0 67.9zM284.2 99.8L21.6 362.4.4 483.9c-2.9 16.4 11.4 30.6 27.8 27.8l121.5-21.3 262.6-262.6c4.7-4.7 4.7-12.3 0-17l-111-111c-4.8-4.7-12.4-4.7-17.1 0zM124.1 339.9c-5.5-5.5-5.5-14.3 0-19.8l154-154c5.5-5.5 14.3-5.5 19.8 0s5.5 14.3 0 19.8l-154 154c-5.5 5.5-14.3 5.5-19.8 0zM88 424h48v36.3l-64.5 11.3-31.1-31.1L51.7 376H88v48z"/></svg>. To get PDF of slides, download HTML, open in Google Chrome, then print to PDF. --- ## Learning outcomes - Identify the different components of RStudio. - Declare variables in R. - Identify common data types and structures used in R. - Recognize and use functions. - Install and load R packages. - Interpret documentation for functions and packages. --- ## Why [R](https://cran.rproject.org/)? <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:FireBrick;overflow:visible;position:relative;"><path d="M497.9 142.1l-46.1 46.1c-4.7 4.7-12.3 4.7-17 0l-111-111c-4.7-4.7-4.7-12.3 0-17l46.1-46.1c18.7-18.7 49.1-18.7 67.9 0l60.1 60.1c18.8 18.7 18.8 49.1 0 67.9zM284.2 99.8L21.6 362.4.4 483.9c-2.9 16.4 11.4 30.6 27.8 27.8l121.5-21.3 262.6-262.6c4.7-4.7 4.7-12.3 0-17l-111-111c-4.8-4.7-12.4-4.7-17.1 0zM124.1 339.9c-5.5-5.5-5.5-14.3 0-19.8l154-154c5.5-5.5 14.3-5.5 19.8 0s5.5 14.3 0 19.8l-154 154c-5.5 5.5-14.3 5.5-19.8 0zM88 424h48v36.3l-64.5 11.3-31.1-31.1L51.7 376H88v48z"/></svg> - Open source -- - Reproducible research with R Markdown -- - Huge community of developers around the world -- - Custom packages (as of Sep 13, 2021) - 18,177 on [CRAN](https://cran.r-project.org/web/packages/available_packages_by_name.html) (The Comprehensive R Archive Network) - 2,042 on [Bioconductor](https://www.bioconductor.org/packages) - More on individual GitHub accounts ??? Numbers of packages are not testable. --- ## Why [RStudio](https://www.rstudio.com/)? Integrated development environment (IDE) for R - User friendly (particularly for novices) - Customizable visual interface - Integrated file, package, and plot management - Local help pages - Integration with other data science resources like Git/GitHub, Shiny apps, etc. --- class: center middle background-image: url(data:image/png;base64,#../../images/rstudio.png) background-size: cover # A tour of RStudio