First Steps in RStudio

1. The four panes of RStudio

When you open RStudio you see one window split into four areas, called panes. (If you only see three, go to File, then New File, then R Script, and the fourth one appears.)

2. Console or script? Use a script

The Console is like talking: quick, but gone once said. A script is like writing it down: you can rerun it, fix it, and share it. Professionals write almost everything in scripts, because the script is the record of the analysis.

1. Create one: File, then New File, then R Script.
2. Type a line, for example mean(c(2, 4, 6)).
3. Run it: put your cursor on the line and press Ctrl+Enter (Windows/Linux) or Cmd+Return (Mac). The line is sent to the Console and the answer appears there.
4. Save it: Ctrl+S or Cmd+S. Give it a short name without spaces, like first_analysis.R.

3. RStudio Projects: so R always finds your files

Every R session has a working directory: the folder R looks in when you give just a file name. If your file is somewhere else, R says it cannot find it. An RStudio Project fixes this for good: it ties a folder to your work, and whenever you open the project, that folder becomes the working directory automatically.

Make your first project (two minutes)

1. File, then New Project, then New Directory, then New Project.
2. Give it a name (for example penguin_project), choose where it lives, and click Create Project.
3. RStudio restarts inside the project. The Files tab now shows the folder and a .Rproj file.
4. Next time, open the project by double-clicking that .Rproj file (or File, then Open Project).

getwd()                              # check: it should print your project folder
my_data <- read.csv("data/my_file.csv")   # a path that starts from the project folder

4. Packages: install once, load every time

A package is a bundle of extra functions someone else wrote, like the tidyverse or DESeq2. Using one takes two different steps, and mixing them up is a classic beginner trap.

install.packages("palmerpenguins")   # ONCE, in the Console (note the quotes)
library(palmerpenguins)              # EVERY session, at the top of your script

5. Getting help

Nobody remembers every function. Professionals look things up all day. R has a help page for every function, and RStudio shows it in the Help tab.

?mean                       # the help page for mean()
help(mean)                  # the same thing, written out
example(mean)               # run the examples at the bottom of the help page
??"standard deviation"     # search all help pages for a phrase

Help pages look dense, but you only need to read three parts at first:

6. Your first errors, and what they mean

Errors are not a sign you are bad at this. Experienced programmers see them all day; they have just learned to read them. Each box below contains a deliberate mistake. (In RStudio the same errors look slightly longer, for example Error in mena(c(2, 4, 6)) : could not find function "mena"; the part after the colon is what matters.) Press Run, read the error and the yellow hint, then fix the code and Run again. (These boxes run real R in your browser; the first Run downloads it, so allow up to a minute.)

A three-step routine for any error

1. Read the last line of the red text. It is usually the useful part.
2. Check the usual suspects on that line and the line above: spelling and capitals, commas, matching brackets and quotes, and whether a needed library() ran.
3. Still stuck? Restart R (Session, then Restart R), rerun your script from the top, and if it still fails, search the exact message.

Practice: fix the broken script

This code has three mistakes. Fix them one at a time, pressing Run after each fix, and let the error messages guide you. One tip: R sometimes points at the line after the real mistake. If the line it names looks fine, check that the line above closed all its brackets. Press Reset to start over.

my_genes <- c("TP53", "BRCA1", "EGFR")     # 1. missing comma after "BRCA1"
gene_lengths <- c(19.1, 81.2, 188.3)       # 2. missing closing bracket
mean(gene_lengths)                         # 3. lowercase g, to match the name
# [1] 96.2

Check your understanding