I have a data frame A with observations
Var1 Var2 Var3 1 3 4 2 5 6 4 5 7 4 5 8 6 7 9
Using data.table you could do an anti-join as follows:
library(data.table) setDT(df1)[!df2, on = names(df1)]
which gives the desired result:
Var1 Var2 Var3 1: 4 5 7 2: 4 5 8 3: 6 7 9