Lab 1: Introduction to R

Please read the document R-intro.pdf. A good tutorial on R is available at www3. In this lab, we will go through the following topics in R.

• Getting help: google, manual, or ?

• Numbers, vectors, and matrix, list

• Math functions

• String

• Reading data from files

• Generating random numbers

• Loops

• Writing your own functions

Installing R

Downloading R at https://cran.microsoft.com/ and following the instruction to install R on your computer. It is highly recommended to install RStudio available at https://posit.co/downloads/ and run R in RStudio. Alternatively, you may run R remotely at https://www.w3schools.com/r/r_intro.asp.

Getting help

• Google search “how to calculate average in R”

• Read the R manual

• Using ? in R

Assignments

We may use “=” or “<-” to assign values to variables. For example, we here generate a variable \(x\) whose value is 3.

x <- 3 
x

3

We may generate a vector variable and use “[i]” to locate elements in the vector.

x <- 2:5 
x
x[2]

1. 2
2. 3
3. 4
4. 5

3

We may generate a string variable which is a vector of characters

x <- "I am a student" 
x
x[3]

'I am a student'

NA

We may generate a matrix variable and use “[i,j]” to locate elements in the vector.

x <- matrix(1:12, nrow=3, ncol=4)
x
x[1,2]
x[1,]
x[,2]

A matrix: 3 × 4 of type int

1	4	7	10
2	5	8	11
3	6	9	12

4

1. 1
2. 4
3. 7
4. 10

1. 4
2. 5
3. 6

A list variable may contain different types of data

x <- list() 
x[[1]] = "I am a student"
x[[2]] = 123
x

1. 'I am a student'
2. 123

Math functions

x=1:3
x*4 
exp(x) 
log(x) 
x=matrix(1,3,3) 
y=matrix(2,3,3) 
x%*%y 
x*y 

1. 4
2. 8
3. 12

1. 2.71828182845905
2. 7.38905609893065
3. 20.0855369231877

1. 0
2. 0.693147180559945
3. 1.09861228866811

A matrix: 3 × 3 of type dbl

6	6	6
6	6	6
6	6	6

A matrix: 3 × 3 of type dbl

2	2	2
2	2	2
2	2	2

Functions for strings

x= rep("",3) 
x[1]  = "I am a graduate student"
x[2] = "who am I?" 
x[3] = "who are you?" 

nchar(x[1]) 
substring(x[1],1,3) 
strsplit(x[2], split=" ") 
paste("a","hello",sep="") 
grep("who",x) 
gsub("graduate","undergraduate",x) 
toupper(x) 
tolower(x)

23

'I a'

1. 1. 'who'
   2. 'am'
   3. 'I?'

'ahello'

1. 2
2. 3

1. 'I am a undergraduate student'
2. 'who am I?'
3. 'who are you?'

1. 'I AM A GRADUATE STUDENT'
2. 'WHO AM I?'
3. 'WHO ARE YOU?'

1. 'i am a graduate student'
2. 'who am i?'
3. 'who are you?'

Reading data from files

data=read.csv("https://book.phylolab.net/binf8441/data/lab1_data.csv") 
data
data[,1] = data[,1] * 10 
write.csv(data,"newdata.csv", row.names=F) 

A data.frame: 25 × 4

V1	V2	V3	V4
<dbl>	<dbl>	<dbl>	<dbl>
0.85332781	0.74786829	0.46077603	0.15329363
0.64914341	0.72662991	0.54947333	0.24407450
0.18542226	0.26383824	0.57954435	0.97183043
0.49988644	0.93933958	0.21200122	0.99106874
0.26374177	0.98626354	0.54450177	0.26758020
0.61112732	0.33217895	0.05834972	0.54131304
0.36914234	0.08085834	0.05588211	0.85876284
0.25350728	0.83706713	0.63014817	0.18264769
0.20357072	0.25849346	0.30214484	0.05598072
0.47116464	0.67394962	0.28081747	0.50700250
0.65012395	0.01026046	0.54948944	0.29967572
0.75223667	0.07775317	0.71929115	0.69480813
0.49442723	0.49138378	0.78043093	0.17591590
0.15364556	0.16670729	0.73303867	0.01809015
0.68046732	0.44405894	0.07383923	0.34538734
0.70716893	0.02882177	0.84202571	0.77440232
0.83129505	0.08661298	0.74557430	0.93672425
0.08638216	0.78741956	0.63246397	0.19764044
0.75538823	0.09585979	0.90368484	0.06294819
0.23711352	0.35896511	0.87965262	0.59115317
0.31184167	0.75218984	0.27041038	0.07943309
0.64790627	0.05523584	0.34259154	0.11879538
0.73803657	0.61349332	0.27953861	0.26276163
0.06645320	0.70710992	0.15588645	0.29456163
0.92541098	0.22925642	0.71822735	0.66264051

Flow control

x=1 
y=2 

x==y 

x != y 

(x==1) || (y==2) 

(x==0) && (y==2) 

FALSE

TRUE

TRUE

FALSE

Loops

x = runif(10, min=0, max=1) 
x
sum=0 
for(i in 1:10){
    sum=sum+x[i]
} 
sum 

1. 0.704896704759449
2. 0.904335947241634
3. 0.395604153163731
4. 0.789092040620744
5. 0.391858619637787
6. 0.919142392696813
7. 0.200044394237921
8. 0.38271605479531
9. 0.725150769110769
10. 0.193563073175028

5.60640414943919

x = 1:10
product = 1 
for(i in 1:10){
    product=product*x[i] 
}
product 

3628800

x = c(5,3,7,2)
n = length(x) 

for(i in 1:(n-1)){ 
    for(j in i:n){ 
        if(x[i]>x[j]){ 
            y=x[i] 
            x[i]=x[j] 
            x[j]=y 
        } 
    } 
} 
x

1. 2
2. 3
3. 5
4. 7

Constructing your own functions

my_function_name = function(x, y, …){

….

return(result)

}

my_sum = function(x){ 
    n = length(x)
    sum=0 
    for(i in 1:n){
        sum = sum + x[i] 
    } 
    sum 
}

x = 1:50
my_sum(x)

1275