Try:
colIndx <- colnames(B)[colnames(B) %in% colnames(A)]
rowIndx <- !as.character(interaction(B)) %in% as.character(interaction(A[colIndx]))
B[rowIndx,]
data
A <- structure(list(V1 = c(1L, 2L, 4L, 1L, 5L), V2 = c(2L, 3L, 5L,
3L, 6L)), .Names = c("V1", "V2"), class = "data.frame", row.names = c(NA,
-5L))
B <- structure(list(V1 = c(1L, 3L, 4L, 1L, 5L, 5L), V2 = c(2L, 4L,
5L, 3L, 7L, 6L)), .Names = c("V1", "V2"), class = "data.frame", row.names = c(NA,
-6L))
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