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

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. Pag<c3><83><c2><a8>s

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"))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Biostrings)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Biostrings/IUPAC_CODE_MAP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IUPAC_CODE_MAP
> ### Title: The IUPAC Extended Genetic Alphabet
> ### Aliases: IUPAC_CODE_MAP mergeIUPACLetters
> ### Keywords: utilities data
> 
> ### ** Examples
> 
>   IUPAC_CODE_MAP
     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" 
>   some_iupac_codes <- c("R", "M", "G", "N", "V")
>   IUPAC_CODE_MAP[some_iupac_codes]
     R      M      G      N      V 
  "AG"   "AC"    "G" "ACGT"  "ACG" 
>   mergeIUPACLetters(IUPAC_CODE_MAP[some_iupac_codes])
  R   M   G   N   V 
"R" "M" "G" "N" "V" 
> 
>   mergeIUPACLetters(c("Ca", "Acc", "aA", "MAAmC", "gM", "AB", "bS", "mk"))
[1] "M" "M" "A" "M" "V" "N" "B" "N"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>