R Basics - bcb420-2025/Clare_Gillis GitHub Wiki

Notes on Unit 2 - R Basics

Time expected: 4 hours

Actual time: 5 hours

Chapter 2 - Installing R and R Studio

  • Tasks 1 & 2 & 3- Already have R, RStudio, and docker installed
  • Image is set of instructions for building a container (system, packages, etc)
  • Container is instance of an image (like an environment)
  • Anything on the container is erased when the container stops running
  • Volume lets you attach container to file system
  • This maps directory PWD on your computer to /home/rstudio/projects on the container
      -v ${PWD}:/home/rstudio/projects
  • Task 4 - Done!
  • search() - show all packages loaded
  • ls("package:<package></package>")
  • Task 5 - Done!
Chapter 3 Setup R to work with it
  • Task 6 - Done!
  • Task 7 - Done!
  • Task 8 - Done!
Chapter 5 Getting help for R
  • Task 9 - Done!
  • Task 10 - Done!
Chapter 6 Basics of R Syntax
  • Task 11 - Done!
  • Task 12 - Done!
  • You can set alternating column colours using a vector like this
      stripes &lt;- c("red", "grey")
      hist(rnorm(200), col=stripes)

Chapter 7 R scalars and vectors

  • Scalar - single value
  • Vector - sequence of scalars with same type
  • Matrix - vectors with defined (often more than 1) dimensions
  • Data frame - like a spreadsheet with a bunch of vector columns
  • List - general collection of items (scalars, vectors, matrices...)
  • typeof() and class() to get type and class of an obj
  • is.<type></type>() to check if an object is a certain type (ex. list, null...)
  • Task 13 - Done!
  • Vector of mixed type coerces everything to a general consistent type (often character - most general)
  • Negative indices exclude that index
  • To append a 4 to the end of a 3-long vector do x[4] <- 4 or x <- c(x, 4)
  • Task 14 - We're adding the sum of the second-last number in myVec (myVec[length(myVec)]) and the last number in myVec (myVec[length(myVec)]) to the end of myVec - Done!
  • SEMICOLON MEANS NEWLINE!
  • dim(a) <- c(x, y) - x is rows, y is columns
  • rbind - row-bind. cbind - column-bind
  • Task 15 - Done!
Chapter 8 Data frames
  • Task 16 & 17 - file.path("data_files","plasmidData.tsv") doesn't seem to exist in R_Exercise-BasicSetup
Chapter 9 Lists
  • Task 18 - Done!
  • Remember lapply functions, they're helpful
  • Task 19 - Done!
Chapter 10 Subsetting and Filtering R objects
  • Task 20 - remember grep. Done!
  • Need to use apply() to use any() or all()
  • ^ = starts with. $ = ends with.
  • Put brackets around an assignment to assign and print the result
  • Task 21 - Done!
Chapter 11 Control structures of R
  • Use || and && in control structures (| and & are vectorized)
  • ifelse() is vectorized
  • Task 22 - Done!
  • Task 23 - Done!
Chapter 13 The complex number above is the same as in Euler’s identity
  • Task 24 - Done!
  • can do missing(<variable></variable>) to check if argument is missing
  • Task 25 - Done!
  • Task 26 - Done!
Chapter 14 Introduction to R Plots
  • stripchart() for histograms is equivalent to rug() for bivariate data
  • can add text() and points() to hist (ex to add counts and norm distn)
  • Task 27 - Done!
  • plot(), rug(), barplot(), hist(), boxplot()
  • See here for colour pallettes, colour names, fonts, point types, and other plotting style info
Chapter 15 Coding Style
  • MAKE CODE EASY TO READ - be explicit, comment, indent comments to align properly
  • <- not = for assignment
  • use for (i in seq(along=x)) not for (i in 1:length(x)) - if x is NULL the loop will execute once with an undefined variable
  • use ::() notation for functions
  • Don't change global state
  • 80 chars per line
  • Use headers
  • Use parentheses for math - don't rely on default behaviour
  • 'CamelCaseStyle'
  • isX or hasX = boolean variables
  • findX, doX, getX (ie. verbs) = simple funcitons
  • Pre-allocate objects right size (growing objects is slow)
  • Explicitly assign values to crucial arguments (don't rely on default behaviour)
  • use [END]
  • Task 28 - Done!
[END]
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