CLASS 6 R FUNCTIONS!

Karolina A19106745

Background

All functions in R have at least 3 things:

• A name that we use to call the function
• One or more input arguments
• The body the lines of R code that do the work

Our first function

Let’s write a silly wee function to add some numbers(the input arguments)

add <- function(x, y){
x + y
}

Now we can use this function

add (100, 1)

[1] 101

add(x=c(100, 1, 100), y=1)

[1] 101   2 101

Q. What if I give a multiple element vector to x1 and y

add(x=c(100, 1), y=c(100, 1))

[1] 200   2

Q. What if I give three inputs to the function?

#add(x=c(100, 1), y=1, z=1)

Q. What if I give only one input to the add function?

addnew<- function(x, y=1){
x + y
}

addnew(x=100)

[1] 101

addnew(c(100,1), 100)

[1] 200 101

If we write our function with input arguments having default value then the user does not have to use a user specified value.

A second function

Let’s try something more interesting: Make a sequence generating tool..

The sample() function can be a useful starting point here:

sample(1:10, size=4)

[1] 9 8 5 2

Q. Generate 9 random numbers taken from the input vector x=1:10?

sample(1:10, size=9)

[1]  6  5  2  3 10  4  9  1  8

Q. Generate 12 random numbers taken from the input vector x=1:10?

#sample(1:10, size=12)

sample(1:10, size=12, replace=TRUE)

 [1] 8 9 6 7 9 6 3 2 2 7 9 6

Q. Write code for the sample() function that generates nucleotide sequences of length 6?

sample(x=c("A", "G", "C", "T"), size=6, replace=TRUE)

[1] "C" "C" "G" "C" "A" "C"

Q. Write a first function generate_dna() that returns a user specified length DNA sequence:

generate_dna <- function(length) {
  
  sample(x=c("A", "G", "C", "T"), size=length, replace=TRUE)
  
}

generate_dna(12)

 [1] "A" "G" "A" "G" "C" "A" "T" "T" "C" "T" "A" "C"

Key-Points Every function in R looks fundamentally the same in terms of its structure. Basically 3 things: name, input, and body

name <- function(input){
  
  body
}

Functions can have multiple inputs. These can be required or optional arguments. With optional arguments having a set default value.

Q. Modify and improve our generate_dna() function to return it’s generated sequence in a more standard formt like “AGTAGTA” rather than the vector “A”, “C”, “G”, “A”

generate_dna <- function(length=6, fasta=TRUE) {
  
ans <- sample(x=c("A", "G", "C", "T"), size=length, replace=TRUE)


if(fasta) {
  cat("Single-element vector output")
  ans <- paste(ans, collapse = "")

} else {
  
  cat("Multi-element vector output")
}

  return(ans)  
}

generate_dna()

Single-element vector output

[1] "ACCCCC"

The paste() function - it’s job is to join up or stick together (a.k.a paste) input strings together

paste("alice", "loves R", sep=" ")

[1] "alice loves R"

Flow control means where the R brain goes in your code

good_mood <- TRUE

if(good_mood) {
  
  cat("Great!")
  
  
} else {
  
  cat("Bummer!")
  
}

Great!

good_mood <- FALSE

if(good_mood) {
  
  cat("Great!")
  
  
} else {
  
  cat("Bummer!")
  
}

Bummer!

A Protein generating function

Q. Write a function, called ’generate_protein()`, that generates a user specified length protein sequence

There are 20 natural amino-acids

aa <- c("A", "R", "N", "D", "B", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V")

generate_protein <- function(length) {
  # The amino-acids to sample from 
  aa <- c("A", "R", "N", "D", "B", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V")

  # Draw n-length amino acids to make our sequence
 ans <-  sample(aa, size=length, replace=T)
  ans <- paste(ans, collapse = "")
}

myseq<- generate_protein(42)
myseq

[1] "WQTWDMFRKEIIGHPNLQFPMQYPYPENRTAVITLCHFSBLA"

Q. Use that function to generate random protein sequences between length 6 and 12

generate_protein(6)
generate_protein(7)
generate_protein(8)
generate_protein(9)
generate_protein(10)
generate_protein(11)
generate_protein(12)

for(i in 6:12) {
  
  # FASTA ID line ">id"
  
  cat(">", i, sep="", "\n")
  
  # Our protein sequence line
  cat(generate_protein(i), "\n")
  
}

>6
HLGNBR 
>7
SDLFDWY 
>8
IEADKCWV 
>9
TRCCMIMKM 
>10
YHHVFDACKB 
>11
DFILLNVKNIV 
>12
EAPMGLPHTPQR 

Q. Are any of your sequences unique i.e not found anywhere in nature?

Yes! Amino acids 6 through 12.