R/Translate.R

In coleoguy/tRanslate: Translates DNA or RNA to amino acids

#' Translates a DNA or RNA sequence into amino acids
#'
#' @param x a text string containing a DNA or RNA sequence
#' @return A text string that represents the translated amino acid sequence
#' @examples
#' x <- "ATGTCCTAG"
#' Translate(x)
#' @export
Translate <- function(x){
  if(nchar(x)%%3!=0){
    warning("DNA sequence isn't a multiple of 3 Translate will assume that the first base is in position one")
  }
  table <- matrix(c("TTT","TTC","TTA","TTG",
                    "CTT","CTC","CTA","CTG",
                    "ATT","ATC","ATA","ATG",
                    "GTT","GTC","GTA","GTG",

                    "TCT","TCC","TCA","TCG","CCT","CCC","CCA","CCG","ACT","ACC","ACA","ACG","GCT","GCC","GCA","GCG",
                    "TAT","TAC","TAA","TAG","CAT","CAC","CAA","CAG","AAT","AAC","AAA","AAG","GAT","GAC","GAA","GAG",
                    "TGT","TGC","TGA","TGG","CGT","CGC","CGA","CGG","AGT","AGC","AGA","AGG","GGT","GGC","GGA","GGG",
                    "F","F","L","L","L","L","L","L","I","I","I","M","V","V","V","V",
                    "S","S","S","S","P","P","P","P","T","T","T","T","A","A","A","A",
                    "Y","Y","*","*","H","H","Q","Q","N","N","K","K","D","D","E","E",
                    "C","C","*","W","R","R","R","R","S","S","R","R","G","G","G","G"),64,2)
  dna <- toupper(x)
  dna <- gsub("U", "T", dna)
  codons <- list()
  num.codons <- nchar(dna)/3
  starts <- seq(from=1,by=3, length.out = num.codons)
  for(i in 1:num.codons){
    codons[i] <- substring(dna, starts[i], starts[i]+2)
  }
  result <- c()
  for(i in 1:length(codons)){
    result[i] <- table[table[,1] == codons[[i]] , 2]
  }
  return(paste(unlist(result), sep="", collapse=""))
}