Replacing Values in R - Error Received

Question

So I have a data frame (called gen) filled with nucleotide information: each value is either A, C, G, or T. I am looking to replace A with 1, C with 2, G with 3, and T with 4. When I use the function gen[gen==A] = 1, I get the error:

Error in [<-.data.frame(*tmp*, gen == A, value = 1) : object 'A' not found

I even tried using gen <- replace(gen, gen == A, 1), but it gives me the same error. Does anyone know how to fix this error? If not, is there a package that I can install in R with a program that will convert A, C, G, and T to numeric values?

Thanks

Answer 1

You need to wrap A in quotes or else R looks for a variable named A. If the columns are character vectors:

R> gen = data.frame(x = sample(c("A", "C", "G", "T"), 10, replace = TRUE), y = sample(c("A", "C", "G", "T"), 10, replace=  TRUE), stringsAsFactors = FALSE)
R> gen[gen == "A"] = 1
R> gen
   x y
1  1 1
2  C C
3  G T
4  T T
5  G G
6  G G
7  1 1
8  C C
9  T 1
10 1 1

also 1 way to do all at once

R> library(car)
R> sapply(gen, recode, recodes = "'A'=1; 'C'=2; 'G'=3; 'T'=4")
      x y
 [1,] 1 1
 [2,] 2 2
 [3,] 3 4
 [4,] 4 4
 [5,] 3 3
 [6,] 3 3
 [7,] 1 1
 [8,] 2 2
 [9,] 4 1
[10,] 1 1

If the columns are factors

R> gen = data.frame(x = sample(c("A", "C", "G", "T"), 10, replace = TRUE), y = sample(c("A", "C", "G", "T"), 10, replace=  TRUE))
R> sapply(gen, as.numeric)
      x y
 [1,] 1 1
 [2,] 2 4
 [3,] 1 2
 [4,] 4 1
 [5,] 2 2
 [6,] 1 4
 [7,] 4 3
 [8,] 3 3
 [9,] 2 4
[10,] 4 2