Applying gsub to various columns

You can use apply to apply it to the whole data.frame

apply(x, 2, function(y) as.numeric(gsub("%", "", y)))
     x1 x2 x3
[1,] 10 60  1
[2,] 20 50  2
[3,] 30 40  3

Or, you could try the lapply solution:

as.data.frame(lapply(x, function(y) gsub("%", "", y)))

  x1 x2 x3
1 10 60  1
2 20 50  2
3 30 40  3