RNAString-class {Biostrings} | R Documentation

## RNAString objects

### Description

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

### Details

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

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

### The RNA alphabet

This alphabet is the same as the DNA alphabet, except that `"T"` is replaced by `"U"`. See `?DNA_ALPHABET` for more information about the DNA alphabet. The RNA alphabet is stored in the `RNA_ALPHABET` predefined constant (character vector).

The `alphabet()` function returns `RNA_ALPHABET` when applied to an RNAString 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 a DNAString object.

  `RNAString(x="", start=1, nchar=NA)`: Tries to convert `x` into an RNAString object by reading `nchar` letters starting at position `start` in `x`.

### Accessor methods

In the code snippet below, `x` is an RNAString object.

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

### Display

The letters in an RNAString 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 RNAStringSet class to represent a collection of RNAString objects.

- The XString and DNAString classes.

- `reverseComplement`

- `alphabetFrequency`

- `IUPAC_CODE_MAP`

- `letter`

### Examples

    RNA_BASES
    RNA_ALPHABET
    dna <- DNAString("TTGAAAA-CTC-N")
    rna <- RNAString(dna)
    rna  # 'options(Biostrings.coloring=FALSE)' to turn off coloring

    alphabet(rna)                 # RNA_ALPHABET
    alphabet(rna, baseOnly=TRUE)  # RNA_BASES

    ## When comparing an RNAString object with a DNAString object,
    ## U and T are considered equals:
    rna == dna  # TRUE

[Package Biostrings version 2.60.2 Index]