chartr {Biostrings} | R Documentation

## Replace letters in a sequence or set of sequences

### Description

Replace letters in a sequence or set of sequences.

### Usage

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

    replaceAmbiguities(x, new="N")

### Arguments

`old` | A character string specifying the characters to be replaced.
`new` | A character string specifying the replacements. It must be a single letter for `replaceAmbiguities`.
`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.

`replaceAmbiguities()` is a simple wrapper around `chartr()` that replaces all IUPAC ambiguities with N.

### Value

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

### See Also

- `chartr` in the base package.

- The `replaceAt` function for extracting or replacing arbitrary subsequences from/in a sequence or set of sequences.

- The `replaceLetterAt` function for a DNA-specific single-letter replacement functions useful for SNP injections.

- `IUPAC_CODE_MAP` for the mapping between IUPAC nucleotide ambiguity codes and their meaning.

- `alphabetFrequency` (and `uniqueLetters`) for tabulating letters in (and extracting the unique letters from) a sequence or set of sequences.

- The XString, XStringSet, XStringViews, and MaskedXString classes.

### Examples

    ## ---------------------------------------------------------------------
    ## A BASIC chartr() EXAMPLE
    ## ---------------------------------------------------------------------

    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)

    ## ---------------------------------------------------------------------
    ## replaceAmbiguities()
    ## ---------------------------------------------------------------------

    dna <- DNAStringSet(c("TTTKYTT-GR", "", "NAASACVT"))
    dna
    replaceAmbiguities(dna)

[Package Biostrings version 2.60.2 Index]