DNAString-class: DNAString objects

In Biostrings: Efficient manipulation of biological strings

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.

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. Pag<c3><a8>s

See Also

• The DNAStringSet class to represent a collection of DNAString objects.

• The XString and RNAString classes.

• reverseComplement

• alphabetFrequency

• IUPAC_CODE_MAP

• letter

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

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, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, 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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[1] "A" "C" "G" "T"
 [1] "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K" "V" "H" "D" "B" "N" "-" "+" "."
  13-letter "DNAString" instance
seq: TTGAAAA-CTC-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. 8, 2020, 11:12 p.m.