complement(x, ...)
reverseComplement(x, ...)

## ---------------------------------------------------------------------
## A. SOME SIMPLE EXAMPLES
## ---------------------------------------------------------------------

x <- DNAString("ACGT-YN-")
reverseComplement(x)

library(drosophila2probe)
probes <- DNAStringSet(drosophila2probe)
probes
alphabetFrequency(probes, collapse=TRUE)
rcprobes <- reverseComplement(probes)
rcprobes
alphabetFrequency(rcprobes, collapse=TRUE)

## ---------------------------------------------------------------------
## B. OBTAINING THE MISMATCH PROBES OF A CHIP
## ---------------------------------------------------------------------

pm2mm <- function(probes)
{
    probes <- DNAStringSet(probes)
    subseq(probes, start=13, end=13) <- complement(subseq(probes, start=13, end=13))
    probes
}
mmprobes <- pm2mm(probes)
mmprobes
alphabetFrequency(mmprobes, collapse=TRUE)

## ---------------------------------------------------------------------
## C. SEARCHING THE MINUS STRAND OF A CHROMOSOME
## ---------------------------------------------------------------------
## Applying reverseComplement() to the pattern before calling
## matchPattern() is the recommended way of searching hits on the
## minus strand of a chromosome.

library(BSgenome.Dmelanogaster.UCSC.dm3)
chrX <- Dmelanogaster$chrX
pattern <- DNAString("ACCAACNNGGTTG")
matchPattern(pattern, chrX, fixed=FALSE)  # 3 hits on strand +
rcpattern <- reverseComplement(pattern)
rcpattern
m0 <- matchPattern(rcpattern, chrX, fixed=FALSE)
m0  # 5 hits on strand -

## Applying reverseComplement() to the subject instead of the pattern is not
## a good idea for 2 reasons:
## (1) Chromosome sequences are generally big and sometimes very big
##     so computing the reverse complement of the positive strand will
##     take time and memory proportional to its length.
chrXminus <- reverseComplement(chrX)  # needs to allocate 22M of memory!
chrXminus
## (2) Chromosome locations are generally given relatively to the positive
##     strand, even for features located in the negative strand, so after
##     doing this:
m1 <- matchPattern(pattern, chrXminus, fixed=FALSE)
##     the start/end of the matches are now relative to the negative strand.
##     You need to apply reverseComplement() again on the result if you want
##     them to be relative to the positive strand:
m2 <- reverseComplement(m1)  # allocates 22M of memory, again!
##     and finally to apply rev() to sort the matches from left to right
##     (5'3' direction) like in m0:
m3 <- rev(m2) # same as m0, finally!

## WARNING: Before you try the example below on human chromosome 1, be aware
## that it will require the allocation of about 500Mb of memory!
if (interactive()) {
  library(BSgenome.Hsapiens.UCSC.hg18)
  chr1 <- Hsapiens$chr1
  matchPattern(pattern, reverseComplement(chr1))  # DON'T DO THIS!
  matchPattern(reverseComplement(pattern), chr1)  # DO THIS INSTEAD
}