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

 Introduction to 'R'  Overview Crash Course  Basic Commands Practical  

Slides

 * [[Media:R_Introduction_Fall_2009.pdf]]

Useful online resources

 * R Tutorial from CRAN, other Basic Tutorial
 * R by example
 * R Graphics Tutorial, R GRaph Gallery.

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
 * Write your own functions
 * Write your own functions