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 subclass (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`) plus `"-"` (the gap letter), `"+"` (the hard masking letter), and `"."` (the not a letter or not available letter). It is stored in the `DNA_ALPHABET` predefined constant (character vector).

The `alphabet()` function returns `DNA_ALPHABET` when applied to a DNAString object.

### 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)`: 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, baseOnly=FALSE)`: 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.

### Display

The letters in a DNAString object are colored when displayed by the `show()` method. Set global option `Biostrings.coloring` to FALSE to turn off this coloring.

### Author(s)

H. Pagès

### See Also

- The DNAStringSet class to represent a collection of DNAString objects.

- The XString and RNAString classes.

- `reverseComplement`

- `alphabetFrequency`

- `IUPAC_CODE_MAP`

- `letter`

### Examples

    DNA_BASES
    DNA_ALPHABET
    dna <- DNAString("TTGAAAA-CTC-N")
    dna  # 'options(Biostrings.coloring=FALSE)' to turn off coloring

    length(dna)
    alphabet(dna)                 # DNA_ALPHABET
    alphabet(dna, baseOnly=TRUE)  # DNA_BASES

[Package Biostrings version 2.60.2 Index]