DNAString-class {Biostrings} | R Documentation |
DNAString objects
Description
A DNAString object allows efficient storage and manipulation of a long DNA sequence.
Details
The DNAString class is a direct XString subclass (with no additional slot). Therefore all functions and methods described in the XString man page also work with a DNAString object (inheritance).
Unlike the BString container that allows storage of any single string (based on a single-byte character set) the DNAString container can only store a string based on the DNA alphabet (see below). In addition, the letters stored in a DNAString object are encoded in a way that optimizes fast search algorithms.
The DNA alphabet
This alphabet contains all letters from the
IUPAC Extended Genetic Alphabet (see ?IUPAC_CODE_MAP
)
plus "-"
(the gap letter), "+"
(the hard
masking letter), and "."
(the not a letter or not
available letter).
It is stored in the DNA_ALPHABET
predefined constant (character
vector).
The alphabet()
function returns DNA_ALPHABET
when
applied to a DNAString 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 an RNAString object.
-
DNAString(x="", start=1, nchar=NA)
: Tries to convertx
into a DNAString object by readingnchar
letters starting at positionstart
inx
.
Accessor methods
In the code snippet below, x
is a DNAString object.
-
alphabet(x, baseOnly=FALSE)
: Ifx
is a DNAString object, then return the DNA alphabet (see above). See the corresponding man pages whenx
is a BString, RNAString or AAString object.
Display
The letters in a DNAString 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 DNAStringSet class to represent a collection of DNAString objects.
Examples
DNA_BASES
DNA_ALPHABET
dna <- DNAString("TTGAAAA-CTC-N")
dna # 'options(Biostrings.coloring=FALSE)' to turn off coloring
length(dna)
alphabet(dna) # DNA_ALPHABET
alphabet(dna, baseOnly=TRUE) # DNA_BASES