15.1 Exercise 10: For loop

Create the script “exercise10.R” and save it to the “Rcourse/Module2” directory: you will save all the commands of exercise 10 in that script.
Remember you can comment the code using #.

correction

getwd()
setwd("~/Rcourse/Module2")

1- Write a for loop that iterates over the sequence of numbers 2 to 10 (both included), and prints the square root of each number (function sqrt()).

correction

for(i in 2:10){
    print(sqrt(i))
}

2- Write a for loop that iterates over the sequence of numbers 5 to 15 (both included), and prints a new vector of 2 elements containing the number and its square root

correction

for(i in 5:15){
    veci <- c(i, sqrt(i))
        print(veci)
}

3- Create the following matrix

mat1 <- matrix(rnorm(40), nrow=20)

• Write a for loop that iterates over each row of mat1 and prints the median value of each row.

correction

for(j in 1:nrow(mat1)){
    # extract the row
    rowj <- mat1[j,]
    # compute the median
    medrowj <- median(rowj)
    # print median value in row
    print(medrowj)
}  

# with less lines of code:
for(j in 1:nrow(mat1)){
    # print median value in row
    print(median(mat1[j,]))
}   

2- If statement in for loop

Create the following matrix:

mat4 <- matrix(c(2, 34, 1, NA, 89, 7, 12, NA, 0, 38),
    nrow=5)

Write a for loop that iterates over each row of mat4: if an NA is found, print the row number and the entire row where the NA is found.

correction

for(k in 1:nrow(mat4)){
    # extract row
    rowk <- mat4[k,]
    if(any(is.na(rowk))){
        print(k)
        print(rowk)
    }
}

3- For loop, if statement and regular expression

Create vector vec4 as:

vec4 <- c("Oct4", "DEPP", "RSU1", "Hk2", "ZNF37A", "C1QL1", "Shh", "Cdkn2a")

vec4 contains Human and Mouse gene symbols.

Loop over each element of vec4:

• If the element is a human gene (both characters and numbers; all characters are written in upper-case), print a vector of two elements: the name of the gene and “human gene”.
  
• If the element is a mouse gene (both characters and numbers; only the first character is written in upper-case), print a vector of two elements: the name of the gene and “mouse gene”.
  

Tip 1: Use grep and a regular expression in the if statement !
Tip 2: When grep does not find a match, it returns an element of length 0 !
Tip 3: You can also use grepl: check the help page

How do you get started?

• First, work on the regular expressions: how do you retrieve Human genes only? How do you retrieve Mouse genes only?
• Then, integrate the regular expressions in the if statement.
• Finally, integrate all this in a for loop!

correction

for(gene in vec4){
    if(length(grep(pattern="^[A-Z0-9]+$", x=gene)) != 0){
        print(c(gene, "human gene"))
    }else if(length(grep(pattern="^[A-Z]{1}[a-z0-9]+$", x=gene)) != 0){
        print(c(gene, "mouse gene"))
    }
}

# With grepl
    # grepl returns a logical vector (match or not for each element of x), not the matching elements themselves.
for(gene in vec4){
        if(grepl(pattern="^[A-Z0-9]+$", x=gene)){
                print(c(gene, "human gene"))
        }else if(grepl(pattern="^[A-Z]{1}[a-z0-9]+$", x=gene)){
                print(c(gene, "mouse gene"))
        }
}

# easier way! whenever a lower case character is present: it is from mouse
for(gene in vec4){
        if(length(grep(pattern="[[:lower:]]", x=gene)) != 0){
                print(c(gene, "mouse gene"))
        }else{
                print(c(gene, "human gene"))
        }
}