RNAString objects
An RNAString object allows efficient storage and manipulation of a long RNA sequence.
Unlike the BString container that allows storage of any single string (based on a single-byte character set) the RNAString container can only store a string based on the RNA alphabet (see below). In addition, the letters stored in an RNAString object are encoded in a way that optimizes fast search algorithms.
This alphabet is the same as the DNA alphabet, except that "T"
is replaced by "U". See ?DNA_ALPHABET for more
information about the DNA alphabet.
The RNA alphabet is stored in the RNA_ALPHABET predefined constant
(character vector).
The alphabet() function returns RNA_ALPHABET when
applied to an RNAString object.
RNAString(x="", start=1, nchar=NA):
Tries to convert x into an RNAString object by reading
nchar letters starting at position start in x.
In the code snippet below, x is an RNAString object.
The letters in an RNAString object are colored when displayed by the
show() method. Set global option Biostrings.coloring
to FALSE to turn off this coloring.
H. Pagès
The RNAStringSet class to represent a collection of RNAString objects.
RNA_BASES
RNA_ALPHABET
dna <- DNAString("TTGAAAA-CTC-N")
rna <- RNAString(dna)
rna # 'options(Biostrings.coloring=FALSE)' to turn off coloring
alphabet(rna) # RNA_ALPHABET
alphabet(rna, baseOnly=TRUE) # RNA_BASES
## When comparing an RNAString object with a DNAString object,
## U and T are considered equals:
rna == dna # TRUEPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.