Class 6: R functions

Laura (PID: A17844089)

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  
}

Lets test our function

add(10, 10)

[1] 20

add(10)

[1] 11

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]  6 10  3

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

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

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

s <- generate_dna(15)

Well done you!

s

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

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

s

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

paste(s, collapse="")

[1] "CCATCTTCCAGTGCA"

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

generate_dna(10, fasta=FALSE)

Well done you!

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

generate_dna(10, fasta=TRUE)

Well done you!

[1] "ACACTATGAA"

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", "Q", "E", 
          "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] "WNNHLFCLSW"

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

generate_protein(5)

[1] "EWTQG"

generate_protein(6)

[1] "QLQNLK"

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

Another approach is to write a for() loop to iterate 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 
QCWAGM
> 7 
RNNDRYL
> 8 
NNKMHMKV
> 9 
HDAKPHCDM
> 10 
FQKLLGRIWV
> 11 
WRNNYVYVQFP
> 12 
DWTIPPMAAAWM

sapply(5:12, generate_protein)

[1] "GPPDC"        "KNGRSG"       "WNGWRKN"      "CFGSCAII"     "KYWLCNWQH"   
[6] "LIRYKFNCMW"   "YTICPDCHHHI"  "RNHGDYCTCRGL"

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.