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Qing Jing wrote:
>  library(Biostrings);
>  dnaAlph<-new("BioPatternAlphabet",DNAAlphabet(),c(N="AGCT",
>  B="CGT",D="AGT",H="ACT",K="GT",M="AC",R="AG",S="CG",
>  V="ACG",W="AT",Y="CT"));
> Error in getClass(Class, where =
> topenv(parent.frame())) : 
>        
> "BioPatternAlphabet" is not a defined
> class

[This is a copy/paste of the answer I've already sent to the R-help list]

Hi Qing,


"BioPatternAlphabet" was a class defined in Biostrings 1 (Biostrings
version 1.y.z). In Biostrings 2, the class system has changed and you don't
need to create an instance of the DNA alphabet anymore:

  - To create a DNAString object, just do:

      > mydna <- DNAString("AGG-HCNTT")
      > mydna
        9-letter "DNAString" object
      Value: AGG-HCNTT

  - To get the DNA alphabet, call alphabet() on a DNAString object:

      > alphabet(mydna)
       [1] "A" "C" "G" "T" "M" "R" "S" "V" "W" "Y" "H" "K" "D" "B" "N" "-"

    or, if you don't have a DNAString instance yet:

      > DNA_ALPHABET
       [1] "A" "C" "G" "T" "M" "R" "S" "V" "W" "Y" "H" "K" "D" "B" "N" "-"

    Note that the "DNA alphabet" is the "IUPAC Extended Genetic Alphabet".

  - To get the mapping between the DNA alphabet and the set of ambiguities
    associated to each "extended" letter:

      > 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"

  - For more details, see:

      > ?DNAString

Cheers,

H.