BioPatternAlphabet-class {Biostrings}R Documentation

Class representing alphabets used in patterns for matching biological sequences

Description

Each object of class "BioPatternAlphabet" represents an alphabet for patterns that is used to match a specific type of biological sequence.

Objects from the Class

Objects can be created by calls of the form new("BioPatternAlphabet", baseAlphabet, letters) where letters is a named character vector with the names being single letters not in the base alphabet and the value corresponding to each name are strings made of letters from the base alphabet. Each such name value pair defines a new letter in the pattern alphabet which matches all the letters in its value string.

Slots

baseAlphabet:
Object of class "BioAlphabet", the base alphabet that for the letters matched by members of this pattern alphabet.
letters:
Object of class "character" representing the letters of the alphabet. Usually roman upper case letters are used. The one exception is the gap character which is always ‘-’.
mapping:
Object of class "integer" representing the encoding used to represent these objects internally.
gap:
Object of class "character", the gap character in the alphabet.

Extends

Class "BioAlphabet", directly.

Methods

BioStringNewValues(alphabet, length.string)
Given alphabet of class "BioPatternAlphabet" return a new uninitialized "BioString" object for that alphabet with length length.string. See BioString-class for more details.
gapletter(x) <- value
Change the letter representing gaps in x of class "BioPatternAlphabet" to value which must be a single letter not in the base alphabet of x.
initialize(.Object, ...)
Method to initialize an object of class "BioPatternAlphabet". Usually used indirectly via a call to new

Author(s)

Saikat DebRoy

See Also

BioAlphabet-class

Examples

dnaAlph <- new("BioPatternAlphabet",
               DNAAlphabet(), c(N="AGCT",
                                B="CGT",
                                D="AGT",
                                H="ACT",
                                K="GT",
                                M="AC",
                                R="AG",
                                S="CG",
                                V="ACG",
                                W="AT",
                                Y="CT"))
dnaAlph

[Package Biostrings version 1.4.0 Index]