Description Usage Arguments Details Value Author(s) References See Also Examples
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.
1 2 |
x |
A vector of non-empty character strings made of IUPAC letters. |
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.
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.
H. Pag<c3><a8>s
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.
1 2 3 4 5 6 | 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"))
|
Loading required package: BiocGenerics
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Attaching package: 'BiocGenerics'
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clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
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strsplit
A C G T M R W S Y K V
"A" "C" "G" "T" "AC" "AG" "AT" "CG" "CT" "GT" "ACG"
H D B N
"ACT" "AGT" "CGT" "ACGT"
R M G N V
"AG" "AC" "G" "ACGT" "ACG"
[1] "R" "M" "G" "N" "V"
[1] "M" "M" "A" "M" "V" "N" "B" "N"
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