Buenas:
Tal vez esto te sirva:
> m <- matrix(c('a', 'b', 'c', 'a', 'bb', 'abc', 'b', 'ba', 'bc'), ncol = 3)
> m
[,1] [,2] [,3]
[1,] "a" "a" "b"
[2,] "b" "bb" "ba"
[3,] "c" "abc" "bc"
> n <- matrix(c('a', 'b', 'c', 'd', 'a', 'ab', 'abc', 'da', 'b', 'ba', 'bc', 'db'), ncol = 3)
> n
[,1] [,2] [,3]
[1,] "a" "a" "b"
[2,] "b" "ab" "ba"
[3,] "c" "abc" "bc"
[4,] "d" "da" "db"
> mc <- apply(m, 1, paste, collapse=' ')
> mc
[1] "a a b" "b bb ba" "c abc bc"
> nc <- apply(n, 1, paste, collapse=' ')
> nc
[1] "a a b" "b ab ba" "c abc bc" "d da db"
> mc %in% nc
[1] TRUE FALSE TRUE
> i <- 1:3
> i[mc %in% nc]
[1] 1 3Un saludo