DNAString-class: DNAString objects

Description Details The DNA alphabet Constructor-like functions and generics Accessor methods Author(s) See Also Examples

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 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.

Author(s)

H. Pagès

See Also

IUPAC_CODE_MAP, letter, XString-class, RNAString-class, reverseComplement, alphabetFrequency

Examples

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DNA_BASES
DNA_ALPHABET
d <- DNAString("TTGAAAA-CTC-N")
length(d)
alphabet(d)                 # DNA_ALPHABET
alphabet(d, baseOnly=TRUE)  # DNA_BASES

Example output

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, which, which.max, which.min

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
[1] "A" "C" "G" "T"
 [1] "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K" "V" "H" "D" "B" "N" "-" "+" "."
[1] 13
 [1] "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K" "V" "H" "D" "B" "N" "-" "+" "."
[1] "A" "C" "G" "T"

Biostrings documentation built on Nov. 17, 2017, 9:26 a.m.