reverseComplement {Biostrings} | R Documentation

## Sequence reversing and complementing

### Description

Use these functions for reversing sequences and/or complementing DNA or RNA sequences.

### Usage

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

### Arguments

`x` | A DNAString, RNAString, DNAStringSet, RNAStringSet, XStringViews (with DNAString or RNAString subject), MaskedDNAString or MaskedRNAString object for `complement` and `reverseComplement`.
`...` | Additional arguments to be passed to or from methods.

### Details

See `?reverse` for reversing an XString, XStringSet or XStringViews object.

If `x` is a DNAString or RNAString object, `complement(x)` returns an object where each base in `x` is "complemented" i.e. A, C, G, T in a DNAString object are replaced by T, G, C, A respectively and A, C, G, U in a RNAString object are replaced by U, G, C, A respectively.

Letters belonging to the IUPAC Extended Genetic Alphabet are also replaced by their complement (M <-> K, R <-> Y, S <-> S, V <-> B, W <-> W, H <-> D, N <-> N) and the gap (`"-"`) and hard masking (`"+"`) letters are unchanged.

`reverseComplement(x)` is equivalent to `reverse(complement(x))` but is faster and more memory efficient.

### Value

An object of the same class and length as the original object.

### See Also

reverse, DNAString-class, RNAString-class, DNAStringSet-class, RNAStringSet-class, XStringViews-class, MaskedXString-class, `chartr`, `findPalindromes`, `IUPAC_CODE_MAP`

### Examples

    ## ---------------------------------------------------------------------
    ## 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
    }

[Package Biostrings version 2.60.2 Index]