First start R on your computer. How to do this depends on your operating system. If you are on a Linux of Mac OS X system, you would typically execute the command R at the shell prompt.
In this course, we are running R on a Linux server. If you would like to install R on your own computer, you can find the appropriate download for your system here.
When R starts, you should see a text message stating the version of R you are running and some further information, followed by a command-line “prompt” ( >, a greater-than sign). The prompt means that R is waiting for you to type a command. To get a feel for how this works, try out some arithmetic:
> 2 + 3
[1] 5
> 5 * 4 + 10
[1] 30
And some function calls:
> abs(-5)
[1] 5
> sum(1,5,10)
[1] 16
To find out how to use a function, type its name preceded by a question mark:
> ? sin
This will bring up some help documentation for the function. You can use the arrow keys to scroll the help text up and down. Press q to get back to the R prompt.
Now try this:
> a <- 10
This command created an object called a. Objects are an important concept in R (as in many other programming languages), and we will be creating more of them in the RNA-seq exercises. We can inspect an object by just typing its name:
> a
[1] 10
We can also change the value of an object that we’ve created:
> a <- 2 * a
> a
[1] 20
The object a created above is a vector with a single element. To create a vector with several elements, you can use the function c():
> b <- c(1, 2, 10)
> b
[1] 1 2 10
Or the colon operator:
> 1:10
[1] 1 2 3 4 5 6 7 8 9 10
A matrix can be created with the function cbind():
> b <- cbind(1:10, 101:110)
> b
[,1] [,2]
[1,] 1 101
[2,] 2 102
[3,] 3 103
[4,] 4 104
[5,] 5 105
[6,] 6 106
[7,] 7 107
[8,] 8 108
[9,] 9 109
[10,] 10 110
We can then use indices to access selected elements of the matrix:
> b[1,]
[1] 1 101
> b[, 2]
[1] 101 102 103 104 105 106 107 108 109 110
> b[c(5,8), 2]
[1] 105 108
You can find manuals for R and more information on the R web site: http://www.r-project.org/