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
)

[Package XNAString version 1.0.2 Index]