I tried replacing all of the times that B appears with b.
Consider the code below, to do the following:
junk <- data.frame(x <- rep(LETTERS[1:4], 3), y <- letters[1:12])
colnames(junk) <- c("alpha", "value")
this provides:
   alpha value
1   A    a
2   B    b
3   C    c
4   D    d
5   A    e
6   B    f
7   C    g
8   D    h
9   A    i
10  B    j
11  C    k
12  D    l
An initial attempt was to use a for and if statements like so:
for(i in junk$alpha) if(i %in% "B") junk$alpha <- "b"
but this replaces all of the values of junk$alpha with b.
 I know why this is doing this but I can't seem to get it to replace only those cases of junk$alpha where the original value was B.