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\name{IUPAC_CODE_MAP}
\alias{IUPAC_CODE_MAP}
\alias{mergeIUPACLetters}
\title{The IUPAC Extended Genetic Alphabet}
\description{
The \code{IUPAC_CODE_MAP} named character vector contains the mapping from
the IUPAC nucleotide ambiguity codes to their meaning.
The \code{mergeIUPACLetters} function provides the reverse mapping.
}
\usage{
IUPAC_CODE_MAP
mergeIUPACLetters(x)
}
\arguments{
\item{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{
\code{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 (\code{"A"}, \code{"C"}, \code{"G"} or \code{"T"})
associated with the code.
The value returned by \code{mergeIUPACLetters} is an unnamed character
vector of the same length as its argument \code{x} where each element
is an IUPAC nucleotide ambiguity code.
}
\author{H. Pagès}
\references{
\url{http://www.chick.manchester.ac.uk/SiteSeer/IUPAC\_codes.html}
IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE:
Cornish-Bowden (1985) \emph{Nucl. Acids Res.} 13: 3021-3030.
}
\seealso{
\code{\link{DNAString}}, \code{\link{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"))
}
\keyword{utilities}
\keyword{data}
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