chartr {Biostrings} | R Documentation

## Translating letters of a sequence

### Description

Translate letters of a sequence.

### Usage

      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`, `replaceLetterAtLoc`, 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)

[Package Biostrings version 2.8.18 Index]