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 convertx
into an RNAString object by readingnchar
letters starting at positionstart
inx
.
Accessor methods
In the code snippet below, x
is an RNAString object.
-
alphabet(x, baseOnly=FALSE)
: Ifx
is an RNAString object, then return the RNA alphabet (see above). See the corresponding man pages whenx
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.
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