Class06: R Functions

Background

Functions are at the heart of using R. Everything we do involves calling and using functions (from data input, analysis to results output).

All functions in R have at least 3 things:

1. A name the thing we use to call the function.
2. One or more input arguments that are comma seperated
3. The body, lines of code between curly brackets {} that does the work of the function.

A first function

We are going to write a function to add some numbers:

add <- function(x) {
  x + 1
}

Let’s try it out now

add(100)

[1] 101

Will this work?

add(c(100, 200, 300))

[1] 101 201 301

Modify the original function to be more useful and add more than just 1

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

add(100, 10)

[1] 110

log(10, base=10)

[1] 1

add(100)

[1] 101

N.B Input agrguments can be either required or optional. The later have a fall-back default that is specified in the function code with an equals sign.

#add(100, 200, 300)

A second function

All functions in R look like thi s

name <- function(arg) {
  body
}

The sample() function in R randomly selects a specified number of items from a given set of values, with or without replacement.

Q. Return 12 numbers picked randomly from the input 1:10

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

 [1]  6  1 10  8  6  4 10  3  8  6 10  8

Q. Write the code to generate a 12 nucleotide long DNA sequence?

sample(c("A", "C", "G", "T"), size=12, replace = TRUE)

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

Q. Write a first version function called generate_dna() that generates a user specified length n random DNA sequence?

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

generate_dna(10)

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

Q. Modify your function to return a FASTA-like sequence so rather than: [1] “T” “A” “G” “T” “C” “A” “T”, we want “TAGTCAT”.

generate_dna <- function(n) {
  bases <- c("A", "C", "G", "T")
  ans <- sample(bases, size=n, replace=TRUE)
  ans <- paste(ans, collapse= "")
  return(ans)
}

generate_dna(10)

[1] "AAGGAATAAG"

Q. Give the user an option to return FASTA format output sequence or standard multi-element vector format?

generate_dna <- function(n=6, fasta=TRUE) {
  bases <- c("A", "C", "G", "T")
  ans <- sample(bases, size=n, replace=TRUE)
  
  if(fasta) {
    ans <- paste(ans, collapse= "")
    cat("Hello there...")
  }
  else {
    cat("General Kenobi")
  }
  return(ans)
}

generate_dna(10)

Hello there...

[1] "TAGTCACTAT"

generate_dna(10, fasta= F)

General Kenobi

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

A new cool function

Q. Write a function called generate_protein() that generates a user specified length protein sequence in FASTA-like format?

generate_protein <- function(n, fasta = TRUE) {
  aa <- c("A","R","N","D","C","E","Q","G","H","I",
  "L","K","M","F","P","S","T","W","Y","V")
  ans <- sample(aa, size=n, replace=TRUE)
  ans <- paste(ans, collapse = "")
  return(ans)
}

generate_protein(20)

[1] "KDTGMTHHTQKIQNTMEAYQ"

Q. Use your new generate_protein() function to generate sequences between length 6 and 12 amino-acids in length and check if any of these are unique in nature (i.e. found in the NR database at NCBI)?

generate_protein <- function(n, fasta = TRUE) {
  aa <- c("A","R","N","D","C","E","Q","G","H","I",
  "L","K","M","F","P","S","T","W","Y","V")
  ans <- sample(aa, size=n, replace=TRUE)
  ans <- paste(ans, collapse = "")
  return(ans)
}
for(i in 6:12) {
  cat(">", i, sep="", "\n")
  cat(generate_protein(i), "\n")
}

>6
ASCCIF 
>7
HQKYEQW 
>8
WFMITPGI 
>9
ILHSGVPDF 
>10
VEMSHHRPMR 
>11
EQKLQYVTCGW 
>12
HMADVTTVANKF