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 1.2.2 Index]