chartr: Replace letters in a sequence or set of sequences
In Biostrings: Efficient manipulation of biological strings

Description Usage Arguments Details Value See Also Examples

Replace letters in a sequence or set of sequences.

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

replaceAmbiguities(x, new="N")

`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.

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.

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

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.

## ---------------------------------------------------------------------
## 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)