[R] Quickest way to match two vectors besides %in%?

[Pete Cap]

Hello list,

I have two data frames, X (48469,2) and Y (79771,5).

X[,1] contains distinct values of Y[,2].
I want to match values in X[,1] and Y[,2], then take
the corresponding value in [X,2] and place it in
Y[,4].

So far I have been doing it like so:
for(i in 1:48469) {
y[which(x[i,1]==y[,3]),4]<-x[i,2]
}

But it chunks along so very slowly that I can't help
but wonder if there's a faster way, mainly because on
my box it takes R about 30 seconds to simply COUNT to
48,469 in the for loop.

I have already tried using %in%.  It tells me if the
values in X[,1] are IN Y[,2], which is useful in
removing unnecessary values from X[,1].  But it does
not tell me exactly where they match.  which(X[,1]
%in% Y[,2]) does but it only matches on the first
instance.

This is the slowest part of the script I'm working
on--if I could improve it I could shave off some
serious operating time.  Any pointers?

Regards,

Pete