| RNAString-class {Biostrings} | R Documentation |
A RNAString object allows efficient storage
and manipulation of a long RNA sequence.
The RNAString class derives directly from the
BString class (with no additional slot).
All functions and methods described in the
BString man page also work
with a RNAString object (inheritance).
Unlike a BString object that allows storage
of any non-empty string (based on a single-byte character set)
a RNAString object can only store a non-empty string
based on the RNAString alphabet (see below).
In addition, the letters stored in a RNAString object
are encoded in a way that optimizes fast search algorithms.
This alphabet contains all letters from the
IUPAC Extended Genetic Alphabet (see IUPAC_CODE_MAP)
where "T" is replaced by "U"
+ the gap letter "-".
It is stored in the RNA_ALPHABET constant (character vector).
The alphabet method also returns
RNA_ALPHABET when applied to a RNAString
object and is provided for convenience only.
In the code snippet below,
src can be a character vector
or a BString (or derived) object.
RNAString(src):
[TODO: Document me]
H. Pages
BString, IUPAC_CODE_MAP,
DNAString, BStringViews
d <- DNAString("TTGAAAA-CTC-N")
r <- RNAString(d)
alphabet(r)
RNA_ALPHABET