IUPAC_CODE_MAP {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. Pagès

### References

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"))

[Package Biostrings version 2.48.0 Index]