Overview

Teaching: 40 min
Exercises: 20 min

Questions

What are the basic features of the R language?

What are the most common objects in R?

What is a vector in R?

Objectives

Define the following terms as they relate to R: object, assign, call, function, arguments, options.

Create objects and assign values to them in R.

Learn how to name objects.

Save a script file for later use.

Use comments to inform script.

Solve simple arithmetic operations in R.

Call functions and use arguments to change their default options.

Create a custom function.

Inspect the content of vectors and manipulate their content.

Subset and extract values from vectors.

Analyze vectors with missing data.

Creating objects in R

You can get output from R simply by typing math in the console:

3 + 5

[1] 8

12 / 7

[1] 1.714286

However, to do useful and interesting things, we need to assign values to objects. To create an object, we need to give it a name followed by the assignment operator <-, and the value we want to give it:

gc_content <- 43.5

This assigns the GC-content value of 43.5 to the object gc_content.

<- is the assignment operator. It assigns values on the right to objects on the left. So, after executing x <- 3, the value of x is 3. The arrow also looks like a mouth (with tongue), which makes it easy to pronounce as x eats 3. For historical reasons, you can also use = for assignments, but not in every context. Because of the slight differences in syntax, it is good practice to always use <- for assignments.

In RStudio, typing Alt + - (push Alt at the same time as the - key) will write ` <- ` in a single keystroke on a PC, while typing Option + - (push Option at the same time as the - key) does the same on a Mac.

Objects can be given almost any name such as x, chromosome_position, or gene_id. Here are some further guidelines on naming objects:

You want your object names to be explicit and not too long.
They cannot start with a number (2x is not valid, but x2 is).
R is case sensitive, so for example, gc_content is different from GC_content.
There are some names that cannot be used because they are the names of fundamental functions in R (e.g., if, else, for, see here for a complete list). In general, even if it’s allowed, it’s best to not use other function names (e.g., c, T, mean, data, df, weights). If in doubt, check the help to see if the name is already in use.
It’s best to avoid dots (.) within names. Many function names in R itself have them and dots also have a special meaning (methods) in R and other programming languages. To avoid confusion, don’t include dots in names.
It is recommended to use nouns for object names and verbs for function names.
Be consistent in the styling of your code, such as where you put spaces, how you name objects, etc. Styles can include “lower_snake”, “UPPER_SNAKE”, “lowerCamelCase”, “UpperCamelCase”, etc. Using a consistent coding style makes your code clearer to read for your future self and your collaborators. In R, three popular style guides come from Google, Jean Fan and the tidyverse. The tidyverse style is very comprehensive and may seem overwhelming at first. You can install the lintr package to automatically check for issues in the styling of your code.

Objects vs. variables

What are known as objects in R are known as variables in many other programming languages. Depending on the context, object and variable can have drastically different meanings. However, in this lesson, the two words are used synonymously. For more information see: https://cran.r-project.org/doc/manuals/r-release/R-lang.html#Objects

When assigning a value to an object, R does not print anything. You can force R to print the value by using parentheses or by typing the object name:

gc_content <- 43.5  # doesn't print anything
(gc_content <- 43.5)  # but putting parenthesis around the call prints the value of `gc_content`

[1] 43.5

gc_content  # and so does typing the name of the object

[1] 43.5

Now that R has gc_content in memory, we can do arithmetic with it. For instance, we may want to calculate the AT-content:

100 - gc_content

[1] 56.5

We can also change an object’s value by assigning it a new one:

gc_content <- 51
100 - gc_content

[1] 49

This means that assigning a value to one object does not change the values of other objects. For example, let’s store the AT-content in a new object, at_content:

at_content <- 100 - gc_content

and then change gc_content to 62.

gc_content <- 62

What do you think is the current content of the object at_content, 38 or 49?

Saving your code

Up to now, your code has been in the console. This is useful for quick queries but not so helpful if you want to revisit your work for any reason. A script can be opened by pressing Ctrl + Shift + N. It is wise to save your script file immediately. To do this press Ctrl + S. This will open a dialogue box where you can decide where to save your script file, and what to name it. The .R file extension is added automatically and ensures your file will open with RStudio.

Don’t forget to save your work periodically by pressing Ctrl + S.

Comments

The comment character in R is #, anything to the right of a # in a script will be ignored by R. It is useful to leave notes and explanations in your scripts. RStudio makes it easy to comment or uncomment a paragraph: after selecting the lines you want to comment, press at the same time on your keyboard Ctrl + Shift + C. If you only want to comment out one line, you can put the cursor at any location of that line (i.e. no need to select the whole line), then press Ctrl + Shift + C.

Challenge 2.1

What are the values after each statement in the following?

mass <- 47.5            # mass?
age  <- 122             # age?
mass <- mass * 2.0      # mass?
age  <- age - 20        # age?
mass_index <- mass/age  # mass_index?

Functions and their arguments

Functions are “canned scripts” that automate more complicated sets of commands including operations assignments, etc. Many functions are predefined, or can be made available by importing R packages (more on that later). A function usually takes one or more inputs called arguments. Functions often (but not always) return a value. A typical example would be the function sqrt(). The input (the argument) must be a number, and the return value (in fact, the output) is the square root of that number. Executing a function (‘running it’) is called calling the function. An example of a function call is:

gc_content <- sqrt(2345)

Here, the value of 2345 is given to the sqrt() function, the sqrt() function calculates the square root, and returns the value which is then assigned to the object gc_content. This function is very simple, because it takes just one argument.

The return ‘value’ of a function need not be numerical (like that of sqrt()), and it also does not need to be a single item: it can be a set of things, or even a dataset. We’ll see that when we read data files into R.

Arguments can be anything, not only numbers or filenames, but also other objects. Exactly what each argument means differs per function, and must be looked up in the documentation (see below). Some functions take arguments which may either be specified by the user, or, if left out, take on a default value: these are called options. Options are typically used to alter the way the function operates, such as whether it ignores ‘bad values’, or what symbol to use in a plot. However, if you want something specific, you can specify a value of your choice which will be used instead of the default.

Let’s try a function that can take multiple arguments: round().

round(3.14159)

[1] 3

Here, we’ve called round() with just one argument, 3.14159, and it has returned the value 3. That’s because the default is to round to the nearest whole number. If we want more digits we can see how to do that by getting information about the round function. We can use args(round) to find what arguments it takes, or look at the help for this function using ?round.

args(round)

function (x, digits = 0) 
NULL

?round

We see that if we want a different number of digits, we can type digits = 2 or however many we want.

round(3.14159, digits = 2)

[1] 3.14

If you provide the arguments in the exact same order as they are defined you don’t have to name them:

round(3.14159, 2)

[1] 3.14

And if you do name the arguments, you can switch their order:

round(digits = 2, x = 3.14159)

[1] 3.14

It’s good practice to put the non-optional arguments (like the number you’re rounding) first in your function call, and then specify the names of all optional arguments. If you don’t, someone reading your code might have to look up the definition of a function with unfamiliar arguments to understand what you’re doing.

Creating functions

One thing that makes R powerful is the ability to write user-defined functions. Functions not only allow you to reuse arbitrary code chunks, they are also great for structuring your code and making the code more readable.

Let’s create a simple function that converts temperatures from Fahrenheit to Celsius:

fahrenheit_to_celsius <- function(temp_fahrenheit) {
  # Convert Fahrenheit temperature to Celsius
  temp_celsius <- (temp_fahrenheit - 32) * 5 / 9
  return(temp_celsius)
}

We define fahrenheit_to_celsius by assigning it to the output of function. The list of argument names are contained within parentheses. Next, the body of the function – the statements that are executed when it runs – is contained within curly braces ({}). The statements in the body are indented by two spaces, which makes the code easier to read but does not affect how the code operates.

When we call the function, the values we pass to it are assigned to those variables so that we can use them inside the function. Inside the function, we use a return statement to send a result back to whoever asked for it.

Automatic Returns

In R, it is not necessary to include the return statement. R automatically returns whichever variable is on the last line of the body of the function. While in the learning phase, we will explicitly define the return statement.

Let’s try running our function. Calling our own function is no different from calling any other function:

# freezing point of water
fahrenheit_to_celsius(32)

[1] 0

# boiling point of water
fahrenheit_to_celsius(212)

[1] 100

We’ve successfully called the function that we defined, and we have access to the value that we returned.

Challenge 2.2

Write a function that returns the sum of two arguments given to it.
Solution
# Calculate the sum of x and y
add_two_args <- function(x, y) { x + y }

# Call the function
add_two_args(9, 7)
[1] 16

Vectors and data types

A vector is the most common and basic data type in R, and is pretty much the workhorse of R. A vector is composed by a series of values, which can be either numbers or characters. We can assign a series of values to a vector using the c() function. For example we can create a vector of animal weights and assign it to a new object weight_g:

weight_g <- c(50, 60, 65, 82)
weight_g

[1] 50 60 65 82

A vector can also contain characters:

animals <- c("mouse", "rat", "dog")
animals

[1] "mouse" "rat"   "dog"

The quotes around “mouse”, “rat”, etc. are essential here. Without the quotes R will assume objects have been created called mouse, rat and dog. As these objects don’t exist in R’s memory, there will be an error message.

There are many functions that allow you to inspect the content of a vector. length() tells you how many elements are in a particular vector:

length(weight_g)

[1] 4

length(animals)

[1] 3

An important feature of a vector, is that all of the elements are the same type of data. The function class() indicates what kind of object you are working with:

class(weight_g)

[1] "numeric"

class(animals)

[1] "character"

The function str() provides an overview of the structure of an object and its elements. It is a useful function when working with large and complex objects:

str(weight_g)

 num [1:4] 50 60 65 82

str(animals)

 chr [1:3] "mouse" "rat" "dog"

You can use the c() function to add other elements to your vector:

weight_g <- c(weight_g, 90)  # add to the end of the vector
weight_g <- c(30, weight_g)  # add to the beginning of the vector
weight_g

[1] 30 50 60 65 82 90

In the first line, we take the original vector weight_g, add the value 90 to the end of it, and save the result back into weight_g. Then we add the value 30 to the beginning, again saving the result back into weight_g.

We can do this over and over again to grow a vector, or assemble a dataset. As we program, this may be useful to add results that we are collecting or calculating.

An atomic vector is the simplest R data type and is a linear vector of a single type. Above, we saw 2 of the 6 main atomic vector types that R uses: "character" and "numeric" (or "double"). These are the basic building blocks that all R objects are built from. The other 4 atomic vector types are:

"logical" for TRUE and FALSE (the boolean data type)
"integer" for integer numbers (e.g., 2L, the L indicates to R that it’s an integer)
"complex" to represent complex numbers with real and imaginary parts (e.g., 1 + 4i) and that’s all we’re going to say about them
"raw" for bitstreams that we won’t discuss further

You can check the type of your vector using the typeof() function and inputting your vector as the argument.

Vectors are one of the many data structures that R uses. Other important ones are lists (list), matrices (matrix), data frames (data.frame), factors (factor) and arrays (array).

Challenge 2.3

We’ve seen that atomic vectors can be of type character, numeric (or double), integer, and logical. But what happens if we try to mix these types in a single vector?

Answer

R implicitly converts them all to be the same type.
What will happen in each of these examples? (hint: use class() to check the data type of your objects):
  num_char <- c(1, 2, 3, "a")
  num_logical <- c(1, 2, 3, TRUE)
  char_logical <- c("a", "b", "c", TRUE)
  tricky <- c(1, 2, 3, "4")
Why do you think it happens?
Answer

Vectors can be of only one data type. R tries to convert (coerce) the content of this vector to find a “common denominator” that doesn’t lose any information.
How many values in combined_logical are "TRUE" (as a character) in the following example (reusing the 2 ..._logicals from above):
  combined_logical <- c(num_logical, char_logical)
Answer

Only one. There is no memory of past data types, and the coercion happens the first time the vector is evaluated. Therefore, the TRUE in num_logical gets converted into a 1 before it gets converted into "1" in combined_logical.

You’ve probably noticed that objects of different types get converted into a single, shared type within a vector. In R, we call converting objects from one class into another class coercion. These conversions happen according to a hierarchy, whereby some types get preferentially coerced into other types. Can you draw a diagram that represents the hierarchy of how these data types are coerced?

Answer

logical → numeric → character ← logical

Subsetting vectors

If we want to extract one or several values from a vector, we must provide one or several indices in square brackets. For instance:

animals <- c("mouse", "rat", "dog", "cat")
animals[2]

[1] "rat"

animals[c(3, 2)]

[1] "dog" "rat"

We can also repeat the indices to create an object with more elements than the original one:

more_animals <- animals[c(1, 2, 3, 2, 1, 4)]
more_animals

[1] "mouse" "rat"   "dog"   "rat"   "mouse" "cat"

R indices start at 1. Programming languages like Fortran, MATLAB, Julia, and R start counting at 1, because that’s what human beings typically do. Languages in the C family (including C++, Java, Perl, and Python) count from 0 because that’s simpler for computers to do.

Conditional subsetting

Another common way of subsetting is by using a logical vector. TRUE will select the element with the same index, while FALSE will not:

weight_g <- c(21, 34, 39, 54, 55)
weight_g[c(TRUE, FALSE, FALSE, TRUE, TRUE)]

[1] 21 54 55

Typically, these logical vectors are not typed by hand, but are the output of other functions or logical tests. For instance, if you wanted to select only the values above 50:

weight_g > 50   # will return logicals with TRUE for the indices that meet the condition

[1] FALSE FALSE FALSE  TRUE  TRUE

## so we can use this to select only the values above 50
weight_g[weight_g > 50]

[1] 54 55

You can combine multiple tests using & (both conditions are true, AND) or | (at least one of the conditions is true, OR):

weight_g[weight_g > 30 & weight_g < 50]

[1] 34 39

weight_g[weight_g <= 30 | weight_g == 55]

[1] 21 55

weight_g[weight_g >= 30 & weight_g == 21]

numeric(0)

Here, > stands for “greater than”, < stands for “less than”, <= stands for “less than or equal to”, and == stands for “equal to”. The double equal sign == is a test for numerical equality between the left and right hand sides, and should not be confused with the single = sign, which performs variable assignment (similar to <-).

A common task is to search for certain strings in a vector. One could use the “or” operator | to test for equality to multiple values, but this can quickly become tedious. The function %in% allows you to test if any of the elements of a search vector are found:

animals <- c("mouse", "rat", "dog", "cat", "cat")

# return both rat and cat
animals[animals == "cat" | animals == "rat"] 

[1] "rat" "cat" "cat"

# return a logical vector that is TRUE for the elements within animals
# that are found in the character vector and FALSE for those that are not
animals %in% c("rat", "cat", "dog", "duck", "goat") 

[1] FALSE  TRUE  TRUE  TRUE  TRUE

# use the logical vector created by %in% to return elements from animals 
# that are found in the character vector
animals[animals %in% c("rat", "cat", "dog", "duck", "goat")]

[1] "rat" "dog" "cat" "cat"

Challenge 2.4 (optional)

Can you figure out why "four" > "five" returns TRUE?

Answer

When using “>” or “<” on strings, R compares their alphabetical order. Here “four” comes after “five”, and therefore is “greater than” it.

Missing data

As R was designed to analyze datasets, it includes the concept of missing data (which is uncommon in other programming languages). Missing data are represented in vectors as NA.

When doing operations on numbers, most functions will return NA if the data you are working with include missing values. This feature makes it harder to overlook the cases where you are dealing with missing data. You can add the argument na.rm = TRUE to calculate the result as if the missing values were removed (rm stands for ReMoved) first.

heights <- c(2, 4, 4, NA, 6)
mean(heights)

[1] NA

max(heights)

[1] NA

mean(heights, na.rm = TRUE)

[1] 4

max(heights, na.rm = TRUE)

[1] 6

If your data include missing values, you may want to become familiar with the functions is.na(), na.omit(), and complete.cases(). See below for examples.

# Extract those elements which are not missing values.
heights[!is.na(heights)]

[1] 2 4 4 6

# Returns the object with incomplete cases removed. 
# The returned object is an atomic vector of type `"numeric"` (or #`"double"`).
na.omit(heights)

[1] 2 4 4 6
attr(,"na.action")
[1] 4
attr(,"class")
[1] "omit"

# Extract those elements which are complete cases. 
# The returned object is an atomic vector of type `"numeric"` (or #`"double"`).
heights[complete.cases(heights)]

[1] 2 4 4 6

Recall that you can use the typeof() function to find the type of your atomic vector.

Challenge 2.5

Using this vector of heights in inches, create a new vector, heights_no_na, with the NAs removed.

 heights <- c(63, 69, 60, 65, NA, 68, 61, 70, 61, 59, 64, 69, 63, 63, NA, 72, 65, 64, 70, 63, 65)

Use the function median() to calculate the median of the heights vector.
Use R to figure out how many people in the set are taller than 67 inches.

Solution

heights <- c(63, 69, 60, 65, NA, 68, 61, 70, 61, 59, 64, 69, 63, 63, NA, 72, 65, 64, 70, 63, 65)

# 1.
heights_no_na <- heights[!is.na(heights)] 
# or
heights_no_na <- na.omit(heights)
# or
heights_no_na <- heights[complete.cases(heights)]

# 2.
median(heights, na.rm = TRUE)

[1] 64

# 3.
heights_above_67 <- heights_no_na[heights_no_na > 67]
length(heights_above_67)

[1] 6

Now that we have learned how to write scripts, and the basics of R’s data structures, we are ready to introduce data frames and factors.