IUPAC_CODE_MAP          package:Biostrings          R Documentation

The IUPAC Extended Genetic Alphabet

Description:

     The 'IUPAC_CODE_MAP' named character vector contains the mapping
     from the IUPAC nucleotide ambiguity codes to their meaning.

     The 'mergeIUPACLetters' function provides the reverse mapping.

Usage:

         IUPAC_CODE_MAP
         mergeIUPACLetters(x)

Arguments:

       x: A vector of non-empty character strings made of IUPAC
          letters. 

Details:

     IUPAC nucleotide ambiguity codes are used for representing
     sequences of nucleotides where the exact nucleotides that occur at
     some given positions are not known with certainty.

Value:

     'IUPAC_CODE_MAP' is a named character vector where the names are
     the IUPAC nucleotide ambiguity codes and the values are their
     corresponding meanings. The meaning of each code is described by a
     string that enumarates the base letters ('"A"', '"C"', '"G"' or
     '"T"') associated with the code.

     The value returned by 'mergeIUPACLetters' is an unnamed character
     vector of the same length as its argument 'x' where each element
     is an IUPAC nucleotide ambiguity code.

Author(s):

     H. Pages

References:

     <URL: http://www.chick.manchester.ac.uk/SiteSeer/IUPAC_codes.html>

     IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE: Cornish-Bowden
     (1985) _Nucl. Acids Res._ 13: 3021-3030.

See Also:

     'DNAString', 'RNAString'

Examples:

       IUPAC_CODE_MAP
       some_iupac_codes <- c("R", "M", "G", "N", "V")
       IUPAC_CODE_MAP[some_iupac_codes]
       mergeIUPACLetters(IUPAC_CODE_MAP[some_iupac_codes])

       mergeIUPACLetters(c("Ca", "Acc", "aA", "MAAmC", "gM", "AB", "bS", "mk"))

