How to replace characters in a vector in R?-CodePudding

I have been tasked with writing an R function capable of taking a DNA string (s) as input and returning the complementary string on the reverse strand (e.g. "ACGT" returns "TGCA"). The result should look something like this:

     > s <- "CCCTTAG"
     > reverse.dna(s)
     [1] "CTAAGGG"

I currently have the following functions for converting a string to a vector and vice versa, however any attempts I have made to use the replace() or switch() commands to substitute the complementary bases into either the string or vector have been unsuccessful.

     string.to.vec <- function(s) {
        strsplit(s,"") [[1]]

     vec.to.string <- function(v) {
        paste(v,collapse="")

As I have very limited experience using R I was wondering if anyone would be able to help me by suggesting the simplest method to implement this functionality into my function. Thanks!

CodePudding user response：

We may use chartr in combination with stri_reverse

library(stringi)
chartr("ACGT", "TGCA", stri_reverse(s))
[1] "CTAAGGG"

CodePudding user response：

The Bioconductor Biostrings package has functions for DNA strings. We convert s from the question to a DNAString object, run reverseComplement and then convert back to character class. Omit the last conversion if you want to keep it as a DNAString.

library(Biostrings)

s |> DNAString() |> reverseComplement() |> as.character()
## [1] "CTAAGGG"