chartr              package:Biostrings              R Documentation

Translating letters of a sequence

Description:

     Translate letters of a sequence.

Usage:

       ## S4 method for signature 'ANY, ANY, XString':
       chartr(old, new, x)

Arguments:

     old: A character string specifying the characters to be
          translated. 

     new: A character string specifying the translations. 

       x: The sequence or set of sequences to translate. If 'x' is an
          XString, XStringSet, XStringViews or MaskedXString object,
          then the appropriate 'chartr' method is called, otherwise the
          standard 'chartr' R function is called. 

Details:

     See '?chartr' for the details.

     Note that, unlike the standard 'chartr' R function, the methods
     for XString, XStringSet, XStringViews and MaskedXString objects do
     NOT support character ranges in the specifications.

Value:

     An object of the same class and length as the original object.

See Also:

     'chartr', 'replaceLetterAt', XString-class, XStringSet-class,
     XStringViews-class, MaskedXString-class, 'alphabetFrequency',
     'matchPattern', 'reverseComplement'

Examples:

       x <- BString("MiXeD cAsE 123")
       chartr("iXs", "why", x)

       ## ---------------------------------------------------------------------
       ## TRANSFORMING DNA WITH BISULFITE (AND SEARCHING IT...)
       ## ---------------------------------------------------------------------

       library(BSgenome.Celegans.UCSC.ce2)
       chrII <- Celegans[["chrII"]]
       alphabetFrequency(chrII)
       pattern <- DNAString("TGGGTGTATTTA")

       ## Transforming and searching the + strand
       plus_strand <- chartr("C", "T", chrII)
       alphabetFrequency(plus_strand)
       matchPattern(pattern, plus_strand)
       matchPattern(pattern, chrII)

       ## Transforming and searching the - strand
       minus_strand <- chartr("G", "A", chrII)
       alphabetFrequency(minus_strand)
       matchPattern(reverseComplement(pattern), minus_strand)
       matchPattern(reverseComplement(pattern), chrII)

