Basic R

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R reference card

A copy of this will also be handed out during the course:

R reference card

Some basic R commands

Using R as a calculator

Start an R session by typing 'R' in a terminal window on the R server. After R has started, anything you type in the terminal will be evaluated by R after you press return.

For example:

1 + 2

Followed by return, will results in this output:

[1] 3


 1 - 2 

[1] -1

Or multiplication:

 4 * 5

[1] 20

Or division:

20 / 5

[1] 4

Comments in R

Any code that is preceded by # is not evaluated by R. So it is useful for giving comments in lines of code:

# This piece of code calculates the sum of 12 and 57
12 + 57

will result in:

[1] 69

So the line "# This piece of code calculates the sum of 12 and 57" is completely ignored.

Variables in R

You can also store the result in a so-called variable, by using '<-' or '='. Say we want to store the result in a variable called 'gene':

 gene <- 1 + 2

Notice that you don't see the result now. We can still get it though by typing:


Resulting in:

[1] 3


Sometimes it is required to not just store one value in a variable, but to store multiple values. This can be done easily in R by creating a vector.


 vectorExample <- c(10, 20, 30, 40, 50)

If we type


We get all the values:

[1] 10 20 30 40 50

If we just want to know one value, for instance the 4th value, we type the element we want in square brackets:


we get:

[1] 40

Data frames

Vectors can be combined into data frames. Say we have two vectors:

names <- c("Michiel", "Lars", "Stan")
scores <- c(10, 20, 30)

we can create a dataframe containing these vectors:

namesAndScores <- data.frame(names, scores)

The result is basically a matrix of values, in this case with 2 columns named "names" and "scores". To get the first element of the second row, we type:

namesAndScores[2, 1]

We can get a complete row with:

namesAndScores[1, ]

We can get a complete column in all of the following ways (each method is identical):

namesAndScores[ , 2]
namesAndScores[ , "scores"]


A type of variable (object would be a better name) you will encounter often is a list. A list object is literally a list of other variables and objects.

An example is for instance:

 namesAndScores <- list(michiel = 1, lars = 2, stan = 3)

This will create a list named namesAndScores. If you type:


You will see:

[1] 1

[1] 2

[1] 3

The nice thing about a list is that it can be used as a sort of look-up table. If we want to know the score of Lars, we simply type his name in the object:


and get:

[1] 2

We will be using lists in this way a lot.


Built-in functions

A function in R is just like a standard mathematical function: you supply an input value and get back an output value.

There are built-in functions in R, like sum(..). This function simply literally sums the values you supply to the function.

So if we create a vector of numbers first:

 numbers <- c(1, 2, 3, 4, 5)

We can calculate the sum of the values:


we get:

[1] 15

Sometimes you can supply more than one input value to a function. The function plot(..) will plot values in a chart. We can supply a range of x coordinates with corresponding y coordinates. In this example we will first make a vector with 7 x coordinates and 7 y coordinates which are the square of the x coordinates:

x <- c(1, 2, 3, 4, 5, 6, 7)
y <- x * x

which can be plotted like this:

 plot(x, y)

User created functions

You can also create your own functions. We could for instance create a function that calculates the squared value of any number or vector of numbers you supply to it:

squareNumbers <- function(x) {



In these lines of code, you can see the word function, which indicates that the created object squareNumbers is a function. There is on input value specified in this function, namely x. Inside the function, the values found in x are squared with ^2 and returned to the user with return(..).

To test, we first make a vector:

x <- c(1, 2, 3, 4, 5, 6, 7)

If we then use the function:


results will look like this:

[1]  1  4  9 16 25 36 49
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