DNAString-class {Biostrings} | R Documentation

## DNAString objects

### Description

A DNAString object allows efficient storage and manipulation of a long DNA sequence.

### Details

The DNAString class is a direct XString subtype (with no additional slot). Therefore all functions and methods described in the XString man page also work with a DNAString object (inheritance).

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

### The DNA alphabet

This alphabet contains all letters from the IUPAC Extended Genetic Alphabet (see `?IUPAC_CODE_MAP`) + the gap (`"-"`) and the hard masking (`"+"`) letters. It is stored in the `DNA_ALPHABET` constant (character vector). The `alphabet` method also returns `DNA_ALPHABET` when applied to a DNAString object and is provided for convenience only.

### Constructor-like functions and generics

In the code snippet below, `x` can be a single string (character vector of length 1), a BString object or an RNAString object.

  `DNAString(x, start=1, nchar=NA, check=TRUE)`: Tries to convert `x` into a DNAString object by reading `nchar` letters starting at position `start` in `x`.

### Accessor methods

In the code snippet below, `x` is a DNAString object.

  `alphabet(x)`: If `x` is a DNAString object, then return the DNA alphabet (see above). See the corresponding man pages when `x` is a BString, RNAString or AAString object.

### Author(s)

H. Pages

### See Also

`IUPAC_CODE_MAP`, `letter`, XString-class, RNAString-class, `reverseComplement`, `alphabetFrequency`

### Examples

      DNA_ALPHABET
      d <- DNAString("TTGAAAA-CTC-N")
      length(d)
      alphabet(d)

[Package Biostrings version 2.8.18 Index]