RNAString-class {Biostrings}R Documentation

The RNAString class

Description

A RNAString object allows efficient storage and manipulation of a long RNA sequence.

Details

The RNAString class derives directly from the BString class (with no additional slot). All functions and methods described in the BString man page also work with a RNAString object (inheritance).

Unlike a BString object that allows storage of any non-empty string (based on a single-byte character set) a RNAString object can only store a non-empty string based on the RNAString alphabet (see below). In addition, the letters stored in a RNAString object are encoded in a way that optimizes fast search algorithms.

The RNAString alphabet

This alphabet contains all letters from the IUPAC Extended Genetic Alphabet (see IUPAC_CODE_MAP) where "T" is replaced by "U" + the gap letter "-". It is stored in the RNA_ALPHABET constant (character vector). The alphabet method also returns RNA_ALPHABET when applied to a RNAString object and is provided for convenience only.

Constructor-like functions and generics

In the code snippet below, src can be a character vector or a BString (or derived) object.

RNAString(src): Tries to convert src into an RNAString object. src can be a single string (character vector of length 1), a BString object or a DNAString object.

Other functions and generics

In the code snippets below, x must be a BString (or derived) object.

alphabet(x): If x is of class RNAString, return the RNAString alphabet (see above). See the corresponding man pages when x is of class BString, DNAString or AAString.

Author(s)

H. Pages

See Also

IUPAC_CODE_MAP, letter, subBString, BString-class, DNAString-class, BStringViews-class

Examples

  d <- DNAString("TTGAAAA-CTC-N")
  r <- RNAString(d)  # reflects the transcription processus
  alphabet(r)
  RNA_ALPHABET

  ## Note that comparing an RNAString instance with a DNAString
  ## instance is possible (and very fast):
  RNAString("GAAAU") == DNAString("CTTTA")  # TRUE

[Package Biostrings version 2.6.6 Index]