# Imperial College/Courses/Fall2009/Synthetic Biology (MRes class)/'R' Tutorial/Crash Course

Fall 2009 - Synthetic Biology (MRes class)

Introduction to 'R'

## Crash Course in R

### Running 'R'

• > Starting R
• Find and Select 'R' within your Programs list
• > Running 'R' from command line
• Once started, 'R' will open an interactive console.
• You can then type 'R' commands. Remember, 'R' commands are case sensitive.
• Commands are separated either by a semi-colon (‘;’), or by a newline.
• The vertical arrow keys on the keyboard can be used to scroll forward and backward through a command history.
• > Running 'R' From a script (strongly suggested)
• 'R' can runs commands that have been saved in a text file (you can use your prefered text editor)
• Commands are separated either by a semi-colon (‘;’), or by a newline.
• For good practice, comments should be added to the script by using '#', like '# this is my comment'
• to execute the script, type in the 'R' console source("path_to_my_script/my_script.R")

### Exit R

• type q() in 'R' console

### Getting help

• Check online tutorials (see above)
• Type help(command_name) or ?command_name like help(length), ?length

### Objects in R

• > Data Types available
• integer
• numeric
• character
• complex
• logical
• > Data Structures available
• Vectors
• A vector is an ordered collection of elements and is equivalent to a single row or a single column in a spreadsheet. Most vectors are numerical (1,2,3…), but logical vectors (TRUE, FALSE, TRUE…) and vectors of character strings (“apples”, “oranges”, “pears”…) also are possible.
• Matrices and Arrays
• A matrix is a set of vectors extending over two dimensions; an array is a set of vectors extending over two or more dimensions. A matrix, therefore, is a two-dimensional array.
• Factors
• A factor is a vector object used to specify a discrete classification (grouping) of the components of other vectors of the same length. R provides both ordered and unordered factors.
• Lists
• A list is a vector containing different types of elements, such as (1, TRUE, “apples”…)
• Data Frames
• A data frame is a matrix-like object consisting of two or more lists or vectors (or matricies or data frames), each of which contains the same number of elements. The objects in a data frame need not be of the same type.
• > Listing objects in memory
• type objects() in 'R' console.
• > Clearing memory
• type rm(object_name)
• to clear all memory type rm(objects())

### Useful functions

• Generating regular expressions
• seq()
• rep()
• 1:30
• ....