| DNAString-class {Biostrings} | R Documentation |
A DNAString object allows efficient storage
and manipulation of a long DNA sequence.
The DNAString 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 DNAString object (inheritance).
Unlike a BString object that allows storage
of any non-empty string (based on a single-byte character set)
a DNAString object can only store a non-empty string
based on the DNAString alphabet (see below).
In addition, the letters stored in a DNAString 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)
+ the gap letter "-".
It is stored in the DNA_ALPHABET constant (character vector).
The alphabet method also returns
DNA_ALPHABET when applied to a DNAString
object and is provided for convenience only.
In the code snippet below,
src can be a character vector
or a BString (or derived) object.
DNAString(src):
Tries to convert src into a DNAString object.
src can be a single string (character vector of length 1),
a BString object or an RNAString object.
In the code snippets below,
x must be a BString (or derived) object.
alphabet(x):
If x is of class DNAString, return the DNAString
alphabet (see above).
See the corresponding man pages when x is of class
BString, RNAString or code{AAString}.
H. Pages
IUPAC_CODE_MAP,
letter,
subBString,
BString-class,
RNAString-class,
BStringViews-class
DNA_ALPHABET
d <- DNAString("TTGAAAA-CTC-N")
length(d)
alphabet(d)