R Flow Control

R if else Statement

• The syntax of if statement is:

• if else statement
• The syntax of if else statement is:
• Note: The else must be in the same line as the closing braces of the if
statement.
if else Ladder
• The syntax of for this is:

• Only one statement will get executed depending upon the test
expressions.
R switch() Function
• The switch() function in R tests an expression against elements of a list. If
the value evaluated from the expression matches an item from the list, the
corresponding value is returned.

• Here, expression is evaluated and based on this value, the corresponding

item in the list is returned.
• If the value evaluated from expression matches with more than one item of
the list, the switch() function returns the first matched item.
• The expression parameter used in the switch () function can be a string as
well. In this case, the matching named item's value is returned.
R for Loop
• Syntax of for loop

• Here, sequence is a vector and val takes on each of its value during
the loop. In each iteration, statement is evaluated.
R while Loop
• In R programming, while loops are used to loop until a specific condition is
met.

• Here, test_expression is evaluated and the body of the loop is entered if

the result is TRUE.
• The statements inside the loop are executed and the flow returns to
evaluate the test_expression again.
• This is repeated each time until test_expression evaluates to FALSE, in
which case, the loop exits.
R break and next Statement
• In R, the break and next statements are control flow statements used
within loops to control the flow of execution.
break Statement
• A break statement is used inside a loop (repeat, for, while) to stop the
iterations and flow the control outside of the loop.
• In a nested looping situation, where there is a loop inside another
loop, this statement exits from the innermost loop that is being
evaluated.
R break and next Statement
next Statement
• A next statement is useful when we want to skip the current iteration
of a loop without terminating it.
• When the next statement is encountered, the current iteration of the
loop is skipped, and the program moves to the next iteration of the
loop.
R repeat loop
• A repeat loop is used to iterate over a block of code multiple number
of times.
• There is no condition check in repeat loop to exit the loop
• We must ourselves put a condition explicitly inside the body of the
loop and use the break statement to exit the loop. Failing to do so will
result into an infinite loop.
Practice Question
• Check whether a number is an Armstrong number or not.
• An Armstrong number, also known as narcissistic number, is a number that is
equal to the sum of the cubes of its own digits.
• For example, if you have a number like 153, it's an Armstrong number
because 1^3 + 5^3 + 3^3 equals 153.
• E.g. 371 = (3*3*3)+(7*7*7)+(1*1*1)

• Hint: Floor(x)  rounds to the largest integer not greater than x

R Functions
• Functions are used to logically break our code into simpler parts
which become easy to maintain and understand.
• The syntax for writing R function is:

• The statements within the curly braces form the body of the function.
These braces are optional if the body contains only a single
expression.
• Finally, this function object is given a name by assigning it to a
variable, func_name
Named Arguments
• The matching of formal arguments to the actual arguments takes
place in positional order.
• We can also call the function using named arguments.
• When calling a function in this way, the order of the actual arguments
doesn't matter.
Default Values for Arguments
• We can assign default values to arguments in a function in R.
• This is done by providing an appropriate value to the formal argument
in the function declaration.
• The use of default value to an argument makes it optional when
calling the function.
Return Value from Function
• Many times, we will require our functions to do some processing and
return the result. This is accomplished with the return() function in R.
• The syntax of the return() function is:

• Here, expression is evaluated, and its value is stored as the result of

the function.
• The value specified in the return() statement is passed as the output
of the function.
Multiple Returns
• The return() function can return only a single object. If we want to
return multiple values in R, we can use a list (or other objects) and
return it.
Practice Question
• Lets create a function to solve quadratic equations
R Programming Scope
• In R programming, scope refers to the accessibility or visibility of
objects (variables, functions, etc.) within different parts of your code.
• In R, there are two main types of variables: global variables and local
variables.
• Global Variables
• Global variables are those variables which exist throughout the execution of a
program. It can be changed and accessed from any part of the program.
• Local Variables
• Local variables are those variables which exist only within a certain part of a
program like a function, and are released when the function call ends.
R Data Structures
• The base data structures in R are vectors, matrices, arrays, data
frames, and lists.
• The first three, vectors, matrices, and arrays, require all elements to
be of the same type or homogeneous, e.g., all numeric or all
character.
• Data frames and lists allow elements to be of different types or
heterogeneous, e.g., some elements of a data frame may be numeric
while other elements may be character.
• These base structures can also be organized by their dimensionality,
i.e., 1-dimensional, 2-dimensional, or N-dimensional,
Vector
• Vector is a basic data structure in R. It contains elements of the same
type. The data types can be logical, integer, double, character,
complex or raw.
• A vector's type can be checked with the typeof() function.
• Another important property of a vector is its length. This is the
number of elements in the vector and can be checked with the
function length().
How to Create Vector in R
• Vectors are generally created using the c() (combine) function.
• x <- c(1,2,3,4,5)
• x <- 1:7
• seq(1, 3, by=0.2)
• Elements of a vector can be accessed using vector indexing. The
vector used for indexing can be logical, integer or character vector.
• Vector index in R starts from 1
How to modify a vector in R?
• We can modify a vector using the assignment operator.
• If we want to truncate the elements, we can use reassignments.

• How to delete a vector in R?

• We can delete a vector by simply assigning a NULL to it.
Vector Functions
• There are several
functions which can
be used to get
information from
vectors, manipulate
vectors, or inspect
vectors.
Plotting vectors
• One key feature of R is it’s ability to graphically display data (plotting)
R Matrix
• Matrix is a two dimensional data structure in R programming.
• Matrix is similar to vector but additionally contains the dimension
attribute.
• All attributes of an object can be checked with the attributes()
function (dimension can be checked directly with the dim() function).
• A matrix can be created using the matrix() function.
• Dimension of the matrix can be defined by passing appropriate values
for arguments nrow and ncol.
Matrix
• It is possible to name the rows and columns of matrix during creation
by passing a 2 element list to the argument dimnames
• These names can be accessed or changed with two helpful functions
colnames() and rownames().
• Another way of creating a matrix is by using functions cbind() and
rbind() as in column bind and row bind.
• Finally, you can also create a matrix from a vector by setting its
dimension using dim().
How to access Elements of a matrix?
• We can access elements of a matrix using the square bracket []
indexing method.
• Elements can be accessed as var[row, column].
• Here row and column are vectors.
• How to modify a matrix in R?
Transpose a Matrix
• A common operation with matrices is to transpose it. This can be
done with the function t().
Matrix functions
• As for vectors a series of functions exist to work with matrices.
R Lists
• If a vector has elements of different types, it is called a list in R
programming.
• A list is a flexible data structure that can hold elements of different
types, such as numbers, characters, vectors, matrices, and even other
lists.
• We can create a list using the list() function
• The structure of the above list can be examined with the str() function
How to access components of a list?
• Lists can be accessed in similar fashion to vectors.
• Integer, logical or character vectors can be used for indexing.
• Indexing with [ will give us a sublist not the content inside the
component.
• To retrieve the content, we need to use [[.
• An alternative to [[, which is used often while accessing content of a
list is the $ operator.
How to modify a list in R?
• We can change components of a list through reassignment.
• We can choose any of the component accessing techniques discussed
before to modify it.
• How to add components to a list?
• Assign values using new tags and it will pop into action.
• How to delete components from a list?
• We can delete a component by assigning NULL to it.
R Data Frame
• Data frame is a two dimensional data structure in R.
• It is a special case of a list which has each component of equal length.
• Each component forms the column and contents of the component
form the rows.
• We can create a data frame using the data.frame() function.
• Many data input functions of R like, read.table(), read.csv(),
read.delim(), read.fwf() also read data into a data frame  we will
talk later
How to Access Components of a Data Frame?
• Components of the data frame can be accessed like a list or like a
matrix
• We can use either [, [[ or $ operator to access columns of data frame.
• How to modify a Data Frame in R?
• Data frames can be modified like we modified matrices through
reassignment.
• Adding Components to Data Frame
• Rows can be added to a data frame using the rbind() function.
R Factors
• Factor is a data structure used for fields that takes only a predefined,
finite number of values (categorical data).
• For example: a data field such as marital status may contain only values from
single, married, separated, divorced, or widowed.
• In such a case, we know the possible values beforehand and these
predefined, distinct values are called levels.
• We can create a factor using the function factor()
Practice
• Write a R program to create two 2x3 matrix and add, subtract,
multiply and divide the matrixes.
• Write a R program to calculate row sums of a matrix using loops
• Write a R program to calculate row sums of a data frame using loops
Practice
• 1- Create the following data frame:
43 181 M
• mydf: 34 172 F
22 189 M
27 167 F

• With Row names: John, Jessica, Steve, Rachel.

And Column names: Age, Height, Gender
Practice
• Calculate the average age and height in mydf
• Add one row to mydf: Georges who is 53 years old and 168cm tall.
• Change the row names of mydf so the data becomes
anonymous: Use Patient1, Patient2, etc. instead of actual names.
• Create the data frame mydf2 that is a subset of mydf containing
only the female entries.
• Create the data frame mydf3 that is a subset of mydf containing
only entries of males taller than 170.
Practice
• download.file("https://public-
docs.crg.es/biocore/sbonnin/Rcourse/genes_dataframe.RData",
"genes_dataframe.RData")
• Load genes_dataframe.RData in your environment Use the load function.
• Explore data and see what it contains
• change column names
• Select rows for which pvalue_KOvsWT (C3) < 0.05 AND
log2FoldChange_KOvsWT(C2) > 0.5. Store in another object.
• Select from the up object the Zinc finger protein coding genes (i.e. the gene
symbol starts with Zfp  to do this you need to learn grep function. Use
help to learn about it