Biostrings (version 2.40.2)

chartr: 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.

Value

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

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.

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)