How to subtract two comma separated columns in R?

Another option leveraging the function vecsets::vsetdiff which doesn't remove duplicates:

library(dplyr)
library(tidyr)
library(purrr)
library(vecsets)

dt %>% 
  mutate(x = strsplit(ColumnA,","),
         y = strsplit(ColumnB,",")) %>% 
  mutate(z = map2(x,y,vecsets::vsetdiff))

      ColumnA ColumnB                x       y       z
1 A,B,C,A,A,A   A,C,A A, B, C, A, A, A A, C, A B, A, A
2       A,B,C       C          A, B, C       C    A, B

Note that you end up with list columns here (which I created on purpose for this to work), but the data might be easier to work with that way anyway.

sapply(1:nrow(dt), function(i){
    a = dt$ColumnA[i]
    b = unlist(strsplit(dt$ColumnB[i], ","))
    for (x in b){
        a = sub(paste0(x, ",?"), "", a)
    }
    sub(",$", "", a)
})
#[1] "B,A,A" "A,B"