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