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Very quick introduction to R
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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 <http://ftp.sunet.se/pub/lang/CRAN/>`_.

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/