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 convert x into a DNAString object by reading
nchar letters starting at position start in x.
Accessor methods
In the code snippet below, x is a DNAString object.
alphabet(x, baseOnly=FALSE):
If x is a DNAString object, then return the DNA
alphabet (see above).
See the corresponding man pages when x is a
BString, RNAString or AAString object.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Biostrings)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Biostrings/DNAString-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DNAString-class
> ### Title: DNAString objects
> ### Aliases: class:DNAString DNAString-class DNA_BASES DNA_ALPHABET
> ### DNAString
> ### Keywords: methods classes
>
> ### ** Examples
>
> DNA_BASES
[1] "A" "C" "G" "T"
> DNA_ALPHABET
[1] "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K" "V" "H" "D" "B" "N" "-" "+" "."
> d <- DNAString("TTGAAAA-CTC-N")
> length(d)
[1] 13
> alphabet(d) # DNA_ALPHABET
[1] "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K" "V" "H" "D" "B" "N" "-" "+" "."
> alphabet(d, baseOnly=TRUE) # DNA_BASES
[1] "A" "C" "G" "T"
>
>
>
>
>
> dev.off()
null device
1
>