DNAString-class          package:Biostrings          R Documentation

DNAString objects

Description:

     A DNAString object allows efficient storage and manipulation of a
     long DNA sequence.

Details:

     The DNAString class is a direct XString subclass (with no
     additional slot). Therefore all functions and methods described in
     the XString man page also work with a DNAString object
     (inheritance).

     Unlike the BString container that allows storage of any single
     string (based on a single-byte character set) the DNAString
     container can only store a string based on the DNA alphabet (see
     below). In addition, the letters stored in a DNAString object are
     encoded in a way that optimizes fast search algorithms.

The DNA alphabet:

     This alphabet contains all letters from the IUPAC Extended Genetic
     Alphabet (see '?IUPAC_CODE_MAP') + the gap ('"-"') and the hard
     masking ('"+"') letters. It is stored in the 'DNA_ALPHABET'
     constant (character vector). The 'alphabet' method also returns
     'DNA_ALPHABET' when applied to a DNAString object and is provided
     for convenience only.

Constructor-like functions and generics:

     In the code snippet below, 'x' can be a single string (character
     vector of length 1), a BString object or an RNAString object.


      'DNAString(x="", start=1, nchar=NA)': Tries to convert 'x' into a
          DNAString object by reading 'nchar' letters starting at
          position 'start' in 'x'.


Accessor methods:

     In the code snippet below, 'x' is a DNAString object.


      'alphabet(x, baseOnly=FALSE)': If 'x' is a DNAString object, then
          return the DNA alphabet (see above). See the corresponding
          man pages when 'x' is a BString, RNAString or AAString
          object.


Author(s):

     H. Pages

See Also:

     'IUPAC_CODE_MAP', 'letter', XString-class, RNAString-class,
     'reverseComplement', 'alphabetFrequency'

Examples:

       DNA_BASES
       DNA_ALPHABET
       d <- DNAString("TTGAAAA-CTC-N")
       length(d)
       alphabet(d)                 # DNA_ALPHABET
       alphabet(d, baseOnly=TRUE)  # DNA_BASES

