| 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):
Tries to convert src into an RNAString object.
src can be a single string (character vector of length 1),
a BString object or a DNAString object.
In the code snippets below,
x must be a BString (or derived) object.
alphabet(x):
If x is of class RNAString, return the RNAString
alphabet (see above).
See the corresponding man pages when x is of class
BString, DNAString or AAString.
H. Pages
IUPAC_CODE_MAP,
letter,
subBString,
BString-class,
DNAString-class,
BStringViews-class
d <- DNAString("TTGAAAA-CTC-N")
r <- RNAString(d) # reflects the transcription processus
alphabet(r)
RNA_ALPHABET
## Note that comparing an RNAString instance with a DNAString
## instance is possible (and very fast):
RNAString("GAAAU") == DNAString("CTTTA") # TRUE