Introduction To R

Pavan Kumar A
What is R?

 The R statistical programming language is a free open

source package based on the S language
( developed by Bell Labs).
 R was created by Ross Ihaka and Robert Gentleman at
the university of Auckland, New Zealand
 The language is very powerful for writing programs.

 Many statistical functions are already built in.

 Contributed packages expand the functionality to cutting

edge research.
BASIC FEATURES OF R
 R is for data analysis and data visualization tool.
 Visualization in the form of charts, plots and graphs
 It is supported with number of graphical, statistical techniques.

 There are several GUI editors of R language, out of which RGui and Rstudio
are commonly used.
 Common characteristics of R

 Effective and powerful data handling

 Arrays and Matrices related operations
 Graphical representations of the analysis
Basic Features of R – Statistical Features
 R provides various statistical and graphical techniques, such as
 Linear and non-linear modeling,
 Classical statistical tests,
 Time-series analysis,
 Classification, Clustering etc.

 R has various predefined packages. User can also install packages.

 R can generate static graphs. To generate dynamic and interactive graphics,

user has to install additional packages
BASIC FEATURES OF R - PROGRAMMING FEATURES
 R supports following
 Basic Math operations
 Vector Operations
 Matrix Operations
 Some other data structures like data frames and lists.

 It can be used with other programming languages such as Python, Perl, Ruby,
Julia and on Hadoop & Spark
Basic Features of R - Packages

 A Package is a collection of functions and datasets.

 To access the contents of package you have to first install (if it is not in-built)
and load it.
 R provides 2 types of packages

 Standard Packages (in-built) part of R source code

 Contributed Packages (user-defined)
 CRAN (Comprehensive R Archive Network) – Collection on R packages.

 These packages widely used in Finance, Genetics, HPC, Machine Learning,

Medical Imaging, Social Sciences and Spatial Statistics
BASIC FEATURES OF R – GRAPHICAL USER INTERFACE
 Some popular text editors and Integrated Development Environments (IDEs)
that support R programming are
 ConTEXT
 Eclipse
 Emacs (Emacs Speaks Statistics)
 Vim editor
 jEdit
 Rstudio
 WinEdit
GETTING STARTED
 Where to get R?
 Go to www.r-project.org
 Downloads: CRAN (The Comprehensive R Archive Network)
 Set your Mirror: Any of the mirror site can be selected.
GETTING STARTED
 Opening a script.
 This gives you a script window.
Getting Started
 Basic assignment and operations.
 Arithmetic Operations:
 +, -, *, /, ^ are the standard arithmetic operators.

 Matrix Arithmetic.
 * is element wise multiplication

 %*% is matrix multiplication

 Assignment
 To assign a value to a variable use “<-” or “=”
Getting Started
 How to use help in R?
 R has a very good built-in help system.
 If you know which function you want help with simply use ?_______ with the
function in the blank.
 Ex: ?hist.

 If you don‟t know which function to use, then use help.search(“_______”).

 Ex: help.search(“histogram”)
Packages
 Packages are collections of
 R functions,
 Data and
 compiled code in a well-defined format.
 The directory where packages are stored is called the library.

 To access and use the package, it has to be loaded first.

Packages
 R comes with a standard set of packages. Others are available for download
and installation. Once installed, they have to be loaded into the session to be
used.
 To install or add new R packages
 install.packages(“package_name”)
 To load the package
 library(package_name)
 To see default packages on R
 library()
 To see installed packages on R
 installed.packages()
 You can create your own package
CRAN
 It is A Comprehensive R Archive Network, contains many packages which can
be used in many domains like
 Genetics, Bioinformatics
 Finance
 HPC (High Performance Computing)
 Machine Learning
 Medical Imaging
 Big data
 R CONSOLE
 After installing R on the Linux machine. Just type R on the command line
 After R console is opened, it shows some basic information about R, such as R
version, date of release, licensing
R CONSOLE
 In the previous figure, notice “>” symbol.
 This is called R prompt, which allows users to write commands and then press
ENTER key to execute the command.
 To get more information about the console, go to Help->Console.
DEVELOPING A SIMPLE PROGRAM
 Sample program for printing
 Here, we are using the print() function to display “Hello World” on the R
console
>print(“Hello World”)
[1] “Hello World”
Here, we are doing simple math
>2+3
[1] 5
 Code begins with „>‟ symbol and output begins with [1]
QUITTING R
 You can quit an active session of R by entering q() command
 After executing the q() command, the question dialogue box appears asking
whether to save the work space.
HANDLING BASIC EXPRESSIONS
 Anything that you type on R console, it executes immediately on pressing the
ENTER key.
 Basic Arithmetic in R
>12+45+9-7
[1] 59
R executes the expression in the following order
12+45+9=66
66-7=59
Lets look at complex mathematical operation
>18+23/2-5/4*3.5
[1] 25.125
HANDLING BASIC EXPRESSIONS
 To calculate such complex mathematical expressions, R uses BODMAS
(Brackets of Division Multiplication Addition Subtraction)

>18+22/2-4/4*3.5
[1] 25.5

>(18+22/2-4/4)*3.5
[1] 98.875
HANDLING BASIC EXPRESSIONS
 Mathematical Operators in R
 +, -, *, () - Simple Mathematical operations
 pi - Stands for Pie value
 X^Y - X raised to Y
 sqrt(x) - square root of x
 abs(x) - Absolute value of x
 factorial(x) - Factorial of x
 log(x) - logarithm of x
 cos(x), sin(x), tan(x) - Trigonometric functions
DECLARING VARIABLES IN R
 Variables are symbols that are used to contain and store the values.
 Two ways to assign the values

 Using “=” symbol

>MyVar=10
Using “<-” symbol
>MyVar<-10

Here, MyVar is a object and it is assigned with the value 10.

Any of the above mentioned can used to assign the values.
VARIABLE TYPES IN R
 Numbers
 Real numbers
 R organizes numbers in 3 formats
 Scalar : Represents a single number (0 dimensional)

 Vector : Represents row of numbers (1 dimensional)

 Matrix: Represents the table like format (2 dimensional)

 Working with Vectors

 It consists of ordered collection of numbers or strings

 Numerical Vector

 String/character vector
VARIABLE TYPES IN R
 Numeric Vector:
 Vector of numeric values.
 A scalar number is the simplest numeric vector.
 Example:
1.5
## [1] 1.5
 To store it for future use,
X<-1.5
VARIABLE TYPES IN R - VECTORS
 Constructing the numeric and character vectors in R
 The numeric() is used to create a zero vector of given length

 The c() is used to construct the vector (Integer/Character)

 c(10,20,20,30,40)
It is a Numerical/Integer vector


 c(“Hello2”, 20, “Hello4”, 30)

 It is combination of Numerical and Character vector
 c(“Hello1”, “Hello2”, “Hello3”)
 It is a Character vector
VARIABLE TYPES IN R - VECTORS
 Constructing the numeric and character vectors in R
 We can also combine mixture of single-element vectors and multi element
vectors and obtain a vector with the same elements as previously created.
 Example
c(1, 2, c(3, 4, 5))
[1] 1 2 3 4 5
VARIABLE TYPES IN R - VECTORS
Creating the vector using (:) operator


>1:15 (generates numbers form 1 to 15)

> c(1:15)
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

> sum(1:15) ## it sums the numbers from 1 to 15

[1] 120
VARIABLE TYPES IN R
 Strings (characters)
 A string should be specified by using quotes. Both single and double

quotes will work

a <- "hello" ## Assigning a string to variable a
a ## Printing variable a
"hello" ## Output of variable a
b <- c("hello","there") ## Assigning two strings to variable b
b ## Printing variable b
"hello" "there" ## Output of variable b
b[1] ## Printing first element of variable b
"hello” ## Output of variable b[1]
VARIABLE TYPES IN R
 Factors
 Another important way R can store data is in the form of factors
 Example of Factorial data Yes/No, Male/Female, A/B/C/D
VARIABLE TYPES IN R
 Logical Vectors
 In contrast to numeric vectors, a logical vector stores a group of TRUE
or FALSE values.
 The simplest logical vectors are TRUE and FALSE themselves
 A more usual way to obtain a logical vector is to ask logical questions about
R objects.
 For example, we can ask R whether 1 is greater than 2:
1>2
## [1] FALSE
c(1, 2) > 2
## [1] FALSE FALSE
VARIABLE TYPES IN R
 Logical Vectors
 Examples
c(1, 2) > c(2, 1)
## [1] FALSE TRUE
Execution c(1 > 2, 2 > 1)

c(2, 3) > c(1, 2, -1, 3)

## [1] TRUE TRUE TRUE FALSE
Execution c(2 > 1, 3 > 2, 2 > -1, 3 > 3)
VARIABLE TYPES IN R
 Named Vectors
 It is a vector with names corresponding to the elements.
 We can give names to a vector when we create it
x <- c(a = 1, b = 2, c = 3)
x
## a b c
## 1 2 3
EXTRACTING AN ELEMENT
 While [ ] creates a subset of a vector, [[]] extracts an element from a vector.
 Example: A vector is like ten boxes of candy, [] gets you three boxes of candy,
but [[]] opens a box and gets you a candy from it.
 For simple vectors, using [] and [[]] to get one element will produce the same
result.
x <- c(a = 1, b = 2, c = 3)
x["a"]
## a
## 1
x[["a"]]
## [1] 1
EXTRACTING AN ELEMENT
 Example: Extract elements which are greater than certain value
input <- c(21, 44, 69, 9, 12, 16, 19, 224, 261, 300)

input > 220

[1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE
TRUE

input[input > 220]

[1] 224 261 300
VARIABLE TYPES IN R – DATA FRAMES
 Data Frames
 It is the collection of many vectors of different types, stores in single variable
> a<-c(1,2,3,4)
> b<-c(2,4,6,8)
> levels <- factor(c("A","B","A","B"))
> MyDataFrame<-data.frame(a, b, levels)
> MyDataFrame
a b levels
1 1 2 A
2 2 4 B
3 3 6 A
4 4 8 B
TELLING THE CLASS OF VECTORS
 Sometimes we need to tell which kind of vector we are dealing with before
taking an action.
 The class() function tells us the class of any R object:
class(c(1, 2, 3))
## [1] "numeric"
class(c(TRUE, TRUE, FALSE))
## [1] "logical"
class(c("Hello", "World"))
## [1] "character"
TELLING THE CLASS OF VECTORS
 If we need to ensure that an object is indeed a vector of a specific class, we
can use is.numeric, is.logical, is.character, and some other
functions with similar names:

is.numeric(c(1, 2, 3))
## [1] TRUE
is.numeric(c(TRUE, TRUE, FALSE))
## [1] FALSE
is.numeric(c("Hello", "World"))
## [1] FALSE
CONVERTING VECTORS strings <- c("1", "2", "3")
 Different classes of vectors class(strings)
can be coerced to a specific ## [1] "character”
--------------------------
class of vector.
strings + 10
 For example, some data are ## Error in strings + 10: non-numeric
string representation of argument to binary operator
numbers, such as 1 and 20. -------------------------
numbers <- as.numeric(strings)
 We need to convert it to
numbers
numeric representation in ## [1] 1 2 3
order to apply numeric class(numbers)
functions. ## [1] "numeric”
----------------------------
numbers + 10
## [1] 11 12 13
CONVERTING VECTORS as.numeric(c("1", "2", "3", "a"))
 Different classes of vectors ## Warning: NAs introduced by coercion
can be coerced to a specific ## [1] 1 2 3 NA
class of vector. -------------------------
 For example, some data are as.logical(c(-1, 0, 1, 2))
string representation of ## [1] TRUE FALSE TRUE TRUE
numbers, such as 1 and 20. --------------------------
as.character(c(1, 2, 3))
 We need to convert it to
## [1] "1" "2" "3"
numeric representation in
--------------------------
order to apply numeric
as.character(c(TRUE, FALSE))
functions.
## [1] "TRUE" "FALSE"
CALLING FUNCTIONS IN R
 Many predefined functions are there in R.
 To invoke, user has to type their names

 For example
> sum(10,20,30)
1] 60
> rep("Hello",3)
[1] "Hello" "Hello" "Hello“
> sqrt(100)
[1] 10
> substr("example",2,4)
[1] "xam"
CREATING AND USING OBJECTS
R uses objects to store the results of a computation
> myobj<-25+12/2-16+(7*pi/2) Assigns a mathematical
> myobj Invokes the myobj object expression to an object
called myobj
[1] 25.99557

 R is case sensitive – that is, it treats data15 and Data15 as completely

different objects.
CREATING AND USING OBJECTS
 An object can be assigned a set of numbers, as for example:
> x12 <- c(10,6,8)
> x12
[1] 10 6 8

 Operations can then be performed on the whole set of numbers.

 For example, for the object x12 created above, check the results of the
following:
> x12 * 10
[1] 100 60 80
READING DATASETS
 Using the c() command:
 c() function is used to combine or concatenate two or more values. Here
example shown is concatenating 2 numerical vectors.
 Syntax for the c() command
HANDLING DATA IN R WORKSPACE
 Handling Workspace includes following
 Using the working directory
 Inspecting the working environment
 Modifying global options
 Managing the library of packages
HANDLING DATA IN R WORKSPACE
 Handling Workspace includes following
 Using the working directory
 The directory in which R is running is called the working directory of

the R session.
 When you access other files on your hard drive, you can use either
absolute paths (for example, D:\Workspaces\test-project\data\2015.csv)
 In an R terminal, you can get the current working directory of the
running R session using getwd()
INSPECTING THE ENVIRONMENT
 In R, every expression is evaluated within a specific environment.
 An environment is a collection of symbols and their bindings.

 If you type commands in the RStudio console, your commands are evaluated
in the Global Environment.
 Example:

 If we run x <- c(1, 2, 3), the numeric vector c(1, 2, 3) is bound to symbol x in
the global environment.
 Global environment has one binding that maps x to integer vector
c(1,2,3)
HANDLING DATA IN R WORKSPACE
The ls() or objects() function is used to return the list of objects in the
workspace
> ls()
[1] "a” "b” "bubba" "fun" "levels" "msg“
[7] "myobj" "n" "x12" "yourname“
The rm() function is used to remove the variables that are not required
anymore in a session
> rm(a)
> ls()
[1] "b“ "bubba” "fun“ "levels” "msg” "myobj" "n"
[8] "x12" "yourname”
HANDLING DATA IN R WORKSPACE
getwd() function: Function used to display the current working directory of
the user
> getwd()
[1] "/home/bioinfo/pavank/rstudio-0.99.489/bin"

save() function: Function used to save the objects created in the active
session.
> save(x12, file="x12.rda")
 It will save in the current working directory with the name “x12.rda”
 You can also save entire working image save.image()
HANDLING DATA IN R WORKSPACE
load() function : Function used to retrieve the saved data
yourname<-"mary“
> ls()
[1] "b” "fun” "levels” "msg” "myobj” "n” "x12” "yourname"
> save(yourname, file="yourname.rda")
> rm(yourname)
> ls()
[1] "b” "fun” "levels" "msg” "myobj” "n” "x12“
> load("yourname.rda")
> ls()
[1] "b” "fun” "levels” “msg” "myobj” "n” "x12” "yourname”
Executing R Scripts
 Creating and Executing R script on Windows:
 Open Notepad, and write R commands
 Save it has “filename.R”
 From the Rgui, file->Open script. It opens a window for browsing the Rscript
 Click Open
EXECUTING R SCRIPTS
 Creating and Executing R script on Linux:
 R script is the series of commands written and saved in .R extension
 To run a script “/home/bioinfo/pavank/R/use1.R”

 You may either use:

 From R Shell
source("/home/bioinfo/pavank/R/use1.R")
 On the Linux Shell
R CMD BATCH /home/bioinfo/pavank/R/use1.R (OR)
Rscript use1.R
ACCESSING HELP AND DOCUMENTATION IN R
 Function used to get help pages of the in-built functions are help() and
example()
> help(ls) or ?ls()
> example(ls) – It shows the examples of ls function

 Sample datasets : R has many in-built datasets

> data()
USING BUILT-IN DATASETS IN R
 There many built-in data sets which can be viewed by data() command. The
output is shown
>data() ##Generates the list of built-in datasets
Using Built-in Datasets in R
 There is a command for viewing all the data sets that are user-built or
contributed packages.
data(package = .packages(all.available = TRUE))
data(package='boot')
THANK YOU !!!