This is the course handbook for WolfWorks: Reproducible Research with R.

Pre-course setup

This lesson assumes that you have current versions of the following installed on your computer:

  1. the R software itself, and
  2. RStudio Desktop.

R and RStudio require separate downloads and installations. R itself refers to the underlying language and computing environment required to write and read this language. RStudio is a graphical integrated development environment which essentially makes running R much easier and more interactive.


Download the most up-to-date versions of R and RStudio onto your system.

If you are working on a Windows system


If you already have a version of R and RStudio installed on your Windows system:
R itself

  • To check which version of R you are running, start RStudio and look at the information printed in the console. The first line should state “R version x.x.x (date of install)”. Alternatively, type sessionInfo() to display the version of R that RStudio is currently running.
  • To confirm whether this version of R is the most current version, visit the CRAN website. If a more recent version of R is available, install it.
  • Although not necessary, if you wish to remove old versions of R from your system, see here for additional information.

RStudio

  • Open RStudio and click on “Help” > “Check for updates”.
  • If a new version of RStudio is available, quit RStudio and download the latest version [see below].

If you do not yet have R and RStudio installed on your Windows system:
R itself

RStudio

  • Go to the RStudio download page and under All Installers select RStudio xxxx.yy.zz-uuu.EXE - Windows 10/11 (where x, y, z and u represent version numbers). Double click the file to install it.
  • Once installed, open RStudio to ensure that it works and you don’t have any error messages. Check that the R version is as expected (the most up to date according to the CRAN website).
If you are working on a MacOS system


If you already have a version of R and RStudio installed on your MacOS system:
R itself

  • To check which version of R you are running, start RStudio and look at the information printed in the console. The first line should state “R version x.x.x (date of install)”. Alternatively, type sessionInfo() to display the version of R that RStudio is currently running.
  • To confirm whether this version of R is the most current version, visit the CRAN website. If a more recent version of R is available, install it.
  • Although not necessary, if you wish to remove old versions of R from your system, see here for additional information.

RStudio

  • Open RStudio and click on “Help” > “Check for updates”.
  • If a new version of RStudio is available, quit RStudio and download the latest version [see below].

If you do not yet have R and RStudio installed on your MacOS system:
R itself

  • Download R from the CRAN website by clicking on the .pkg file for the latest release. Make sure you select the correct file depending on whether your mac is an M1/M2 Mac or an older Intel Mac. You can check this on your mac by going to “About this mac” and checking the type of processer you have.
  • Double click on the downloaded file to install R.

RStudio

  • Go to the RStudio download page and under All Installers select RStudio xxxx.yy.zz-uuu.DMG - macOS 10.15+ (where x, y, z and u represent version numbers). Double click the file to install it.
  • Once installed, open RStudio to ensure that it works and you don’t have any error messages. Check that the R version is as expected (the most up to date according to the CRAN website).
If you are working on a Linux system


Installing R and RStudio on a Linux system
R itself

  • Follow the instructions for your distribution from CRAN. For most distributions, you could use your package manager (e.g., for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora run sudo yum install R), but this is not recommended as the versions installed by this approach are typically out of date.

R Studio

  • Go to the RStudio download page and under All Installers select the version that matches your distribution, and install it with your preferred method (e.g., for Debian/Ubuntu sudo dpkg -i rstudio-xxxx.yy.zz-uuu-amd64.deb at the terminal).
  • Once installed, open RStudio to ensure that it works and you don’t have any error messages. Check that the R version is as expected (the most up to date according to the CRAN website).


You also need to download some files to follow this lesson:

  1. Make a new folder in your Desktop called r-training.
  2. Within this folder, create three sub-folders called raw_data, processed_data, and figures.
  3. Download rnaseq.csv and move the file to the raw_data folder.