XNAString-class {XNAString}

R Documentation

Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.

Description

The package inherits some of the functionalities from Biostrings package. In contrary to Biostrings sequences, XNAString classes allow for description of base sequence, sugar and backbone in a single object. XNAString is able to capture single stranded oligonucleotides, siRNAs, PNAs, shRNAs, gRNAs and synthetic mRNAs, and enable users to apply sequence-manipulating Bioconductor packages to their analysis. XNAString can read and write a HELM notation, compute alphabet frequency, align and match targets.

Usage

XNAString(
  name,
  base,
  sugar,
  backbone,
  target,
  conjugate5,
  conjugate3,
  secondary_structure,
  duplex_structure,
  dictionary,
  compl_dictionary,
  default_sugar,
  default_backbone
)

## S4 method for signature 'XNAString'
show(object)

## S4 method for signature 'XNAString'
initialize(
  .Object,
  name,
  base,
  sugar,
  backbone,
  target,
  conjugate5,
  conjugate3,
  secondary_structure,
  duplex_structure,
  dictionary,
  compl_dictionary,
  default_sugar,
  default_backbone
)

seqtype(x)

## S4 method for signature 'XNAString'
seqtype(x)

Arguments

name	string (or character)
base	string (or character), RNAString, RNAStringSet, DNAString or DNAStringSet
sugar	string (or character)
backbone	string (or character)
target	DNAStringSet, DNAString or character
conjugate5	string (or character)
conjugate3	string (or character)
secondary_structure	list
duplex_structure	list
dictionary	data.table with following columns: "HELM", "type", "symbol". By default internal XNAString dictionary is used.
compl_dictionary	data.table with following columns: "base", "target". By default internal XNAString dictionary is used
default_sugar	character, a single letter which will be replicated in sugar slot as default value
default_backbone	character, a single letter which will be replicated in backbone slot as default value
object	XNAString object
.Object	XNAString object
x	A single string specifying the type of sequences

Value

Object which consists of name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary, compl_dictionary.

Author(s)

Anna Gorska

Examples

obj1 <- XNAString(
  base = "ATCG",
  sugar = "FODD",
  conjugate3 = "TAG"
)
obj2 <- XNAString(
  base = "ATCG",
  sugar = "FODD",
  backbone = "SBB"
)
str(obj2)
name(obj2) <- 'a'
base(obj2) <- 'ATTT'
sugar(obj2) <- 'LMFF'
backbone(obj2) <- 'BAB'
conjugate5(obj2) <- 'TFJSJG'
conjugate3(obj2) <- 'ARTSS'
my_dic <- data.table::data.table(type = c(rep('base',3),
                                          rep('sugar',2),
                                          rep('backbone',3)),
                                symbol = c('G', 'E', 'A', 'F',
                                           'O', 'S', 'B', 'X'))
obj1 <- XNAString(base = 'AAE',
                  sugar = 'FFO',
                  backbone='SB',
                  dictionary = my_dic)
obj2 <- XNAString(base = c('EAA', 'AAAA'),
                  sugar = c('FFO', 'OOOO'),
                  name = c('a'),
                  conjugate5 = c('TTT'),
                  dictionary = my_dic)

my_dic <- data.table::data.table(
  type = c(
    rep("base", 3),
    rep("sugar", 2),
    rep("backbone", 3)
  ),
  symbol = c("G", "E", "A", "F", "O", "S", "B", "X")
)
obj1 <- XNAString(
  base = "AAE",
  sugar = "FFO",
  backbone = "SB",
  dictionary = my_dic
)
obj2 <- XNAString(
  base = c("EAA", "AAAA"),
  sugar = c("FFO", "OOOO"),
  name = c("a"),
  conjugate5 = c("TTT"),
  dictionary = my_dic
)

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