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)