Matching up two vectors in R

Question

I have two vectors in R as shown below. The first one represents amino acid numbers with some positions missing while the second one represents the full list. I need to some

Answer 1

to return the indices use %in%

> (a <- letters[1:5])
[1] "a" "b" "c" "d" "e"
> b <- c("a", "b", "e", "f")
> (which(a%in%b))
[1] 1 2 5
> (which(b%in%a))
[1] 1 2 3

Answer 2

Use match:

match(PDBRenum.3V5Q[,2], PDBXPoly.3V5Q[[1]][,3])

With match(x,y), the ith element of the output is the first index of y that matches x[i], unless x[i] doesn't appear in y, in which case it gives NA.

match is most useful when y has no repeated values.

For example:

> match( c(1,3,5), c(2,6,7,3,1) )
[1]  5  4 NA
> match( c(1,3,5), c(2,6,7,3,1, 8,1,3) )
[1]  5  4 NA