BioPatternAlphabet-class {Biostrings} | R Documentation |
Each object of class "BioPatternAlphabet" represents an alphabet for patterns that is used to match a specific type of biological sequence.
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.
baseAlphabet
:"BioAlphabet"
,
the base alphabet that for the letters matched by members of this
pattern alphabet. letters
:"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
:"integer"
representing
the encoding used to represent these objects internally. gap
:"character"
, the gap
character in the alphabet.
Class "BioAlphabet"
, directly.
alphabet
of class "BioPatternAlphabet" return a new uninitialized
"BioString" object for that alphabet with length
length.string
. See BioString-class
for more
details.x
of class "BioPatternAlphabet" to value
which must
be a single letter not in the base alphabet of x
.new
Saikat DebRoy
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