replace a list of values by another in R

Question

I have a dataframe with any of these values.

from=c("A","C","G","T","R","Y","M","K","W", "S","N")

and I want to replace accordingly with

to=c("AA","CC","GG","TT","AG","CT","AC","GT","AT", "CG","NN")

What is the best way to do that , loop over all values to replace? or loop over matrix position. or any other solution?

dd<-matrix(sample(from, 100, replace=TRUE), 10) 

dd
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,] "K"  "S"  "G"  "T"  "R"  "N"  "A"  "C"  "W"  "M"  
 [2,] "Y"  "K"  "S"  "G"  "T"  "R"  "N"  "A"  "C"  "W"  
 [3,] "M"  "Y"  "K"  "S"  "G"  "T"  "R"  "N"  "A"  "C"  
 [4,] "W"  "M"  "Y"  "K"  "S"  "G"  "T"  "R"  "N"  "A"  
 [5,] "C"  "W"  "M"  "Y"  "K"  "S"  "G"  "T"  "R"  "N"  
 [6,] "A"  "C"  "W"  "M"  "Y"  "K"  "S"  "G"  "T"  "R"  
 [7,] "N"  "A"  "C"  "W"  "M"  "Y"  "K"  "S"  "G"  "T"  
 [8,] "R"  "N"  "A"  "C"  "W"  "M"  "Y"  "K"  "S"  "G"  
 [9,] "T"  "R"  "N"  "A"  "C"  "W"  "M"  "Y"  "K"  "S"  
[10,] "G"  "T"  "R"  "N"  "A"  "C"  "W"  "M"  "Y"  "K"

I used loop over all from to to.

myfunc<-function(xx){

  from=c("A","C","G","T","R","Y","M","K","W", "S","N");
  to=c("AA","CC","GG","TT","AG","CT","AC","GT","AT", "CG","NN");
  for (i in 1:11){
      xx[xx==from[i]]<-to[i];
  }
  return(xx);
}

it worked great for small matrix, but takes a long time for big matrix. Any effcient solution?

Thanks

Answer 1

Create a map

map = setNames(to, from)

and go from A to B

dd[] = map[dd]

The map serves as a look-up, associating 'from' names with 'to' values. The assignment preserves matrix dimensions and dimnames.

Answer 2

matrix(to[match(dd,from)], nrow=nrow(dd))

match returns a vector without dimensions, so you need to recreate the matrix.