Class 6: R functions

Blinda Sui (PID: A17117043)

All functions in R have at least 3 things:

• A name, we pick this and use it to call the function.
• Input arguments, there can be multiple comma seperated inputs to the function. The body, lines of R code that do the work of the function.

Our first wee function:

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

Let’s test our function

add(c(1, 2, 3), y=10)

[1] 11 12 13

add(10)

[1] 11

add(10, c(10, 120))

[1]  20 130

A second function

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

The ‘sample()’ function could be useful here.

sample(1:10, size = 3)

[1] 8 5 4

change this to work with the nucleotides A C G and T and return 3 or them.

n <- c("A", "C", "G", "T")
sample(n, size = 15, replace = TRUE)

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

Turn this snipet into a function that returns a user specified length dna sequence. Let’s call it ‘generate_dna()’

generate_dna <- function(len=10, fasta=FALSE){
  n <- c("A", "G", "C", "T")
  v <- sample(n, size=len, replace = TRUE)
  
  # Make a single element vector
  s <- paste(v, collapse = "")
  
  cat("Well done you!\n")
  
  if(fasta) {
    return(s)
  } else {
    return(v)
  }
}

generate_dna(5)

Well done you!

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

s <- generate_dna(15)

Well done you!

s

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

I want the option to return a single element character vector with my sequence all together like this: “GGAGTAC”

s

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

paste(s, collapse = "")

[1] "GATGTTCTTTTGGCC"

generate_dna(10, fasta=TRUE)

Well done you!

[1] "GCACACAGTT"

generate_dna(10, fasta=FALSE)

Well done you!

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

A more advanced example

Make a third function that generates protein sequence of a user specified length and format.

generate_protein <- function(size = 15, fasta = TRUE) {
  aa <- c("A","R","N","D","C","E","Q","G","H","I","L",
         "K","M","F","P","S","T","W","Y","V")
  seq <- sample(aa, size = size, replace = TRUE)
  
  if(fasta) {
    return(paste(seq, collapse = ""))
  } else {
    return(seq)
  }
}

Try this out…

generate_protein(10)

[1] "LEKLPYSNAN"

Q. Generate random protein sequences between lengths 5 and 12 amino-acids.

generate_protein(5)

[1] "MMKHM"

generate_protein(6)

[1] "QFRHCS"

One approach is to do this by brute force calling our unction for each lenght 5 to 12.

Another approach is to write a ‘for()’ loop to itterate over the input valued 5 to 12.

A very useful third R specific approach is to use the ‘sapply()’ function.

seq_lengths <- 6:12
for(i in seq_lengths) {
  cat(">", i, "\n")
  cat(generate_protein(i))
  cat("\n")
}

> 6 
VTQWIQ
> 7 
ERKQLNP
> 8 
YCHTHPAH
> 9 
MNDNCCYII
> 10 
FFKPKKLIDT
> 11 
PAHATCDQDRG
> 12 
DTEMWSEHKFCH

sapply(6:12, generate_protein)

[1] "NHCCIW"       "NLNAPLK"      "YAQSFLLN"     "NIHMMARLK"    "TAYHAKGLQN"  
[6] "VPDVAMRKSPD"  "PIMECIRSGRSP"

Key-Point: Writing functions in R is doable but not the easiest thing. Starting with a working snippet of code and then using LLM tools to improve and generalize your function code is a productive approach.